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	<id>https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?action=history&amp;feed=atom&amp;title=AMBER</id>
	<title>AMBER - Revision history</title>
	<link rel="self" type="application/atom+xml" href="https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?action=history&amp;feed=atom&amp;title=AMBER"/>
	<link rel="alternate" type="text/html" href="https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=AMBER&amp;action=history"/>
	<updated>2026-05-17T23:07:25Z</updated>
	<subtitle>Revision history for this page on the wiki</subtitle>
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	<entry>
		<id>https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=AMBER&amp;diff=2612&amp;oldid=prev</id>
		<title>import&gt;Mp466 at 16:05, 3 October 2009</title>
		<link rel="alternate" type="text/html" href="https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=AMBER&amp;diff=2612&amp;oldid=prev"/>
		<updated>2009-10-03T16:05:51Z</updated>

		<summary type="html">&lt;p&gt;&lt;/p&gt;
&lt;table style=&quot;background-color: #fff; color: #202122;&quot; data-mw=&quot;interface&quot;&gt;
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				&lt;col class=&quot;diff-content&quot; /&gt;
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				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #202122; text-align: center;&quot;&gt;← Older revision&lt;/td&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #202122; text-align: center;&quot;&gt;Revision as of 16:05, 3 October 2009&lt;/td&gt;
				&lt;/tr&gt;&lt;tr&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 15:&lt;/td&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 15:&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Producing a PDB from a coordinates and topology file]] - using &#039;&#039;amdpdb&#039;&#039;&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Producing a PDB from a coordinates and topology file]] - using &#039;&#039;amdpdb&#039;&#039;&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Running GMIN with MD move steps AMBER]]&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Running GMIN with MD move steps AMBER]]&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-empty diff-side-deleted&quot;&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot; data-marker=&quot;+&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Evaluating different components of AMBER energy function with SANDER]]&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Running MD with AMBER]]&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Running MD with AMBER]]&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[REMD with AMBER]]&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[REMD with AMBER]]&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;</summary>
		<author><name>import&gt;Mp466</name></author>
	</entry>
	<entry>
		<id>https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=AMBER&amp;diff=2611&amp;oldid=prev</id>
		<title>import&gt;Mp466 at 11:54, 31 July 2009</title>
		<link rel="alternate" type="text/html" href="https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=AMBER&amp;diff=2611&amp;oldid=prev"/>
		<updated>2009-07-31T11:54:51Z</updated>

		<summary type="html">&lt;p&gt;&lt;/p&gt;
&lt;table style=&quot;background-color: #fff; color: #202122;&quot; data-mw=&quot;interface&quot;&gt;
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				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #202122; text-align: center;&quot;&gt;← Older revision&lt;/td&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #202122; text-align: center;&quot;&gt;Revision as of 11:54, 31 July 2009&lt;/td&gt;
				&lt;/tr&gt;&lt;tr&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 11:&lt;/td&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 11:&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Generating parameters using RESP charges from GAMESS-US]]&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Generating parameters using RESP charges from GAMESS-US]]&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Simple scripts for LEaP to create topology and coordinate files]] &lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Simple scripts for LEaP to create topology and coordinate files]] &lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-empty diff-side-deleted&quot;&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot; data-marker=&quot;+&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Preparing an AMBER topology file for a protein system]] - step by step guide&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Preparing an AMBER topology file for a protein plus ligand system]] - step by step guide&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Preparing an AMBER topology file for a protein plus ligand system]] - step by step guide&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Producing a PDB from a coordinates and topology file]] - using &#039;&#039;amdpdb&#039;&#039;&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Producing a PDB from a coordinates and topology file]] - using &#039;&#039;amdpdb&#039;&#039;&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;</summary>
		<author><name>import&gt;Mp466</name></author>
	</entry>
	<entry>
		<id>https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=AMBER&amp;diff=2610&amp;oldid=prev</id>
		<title>import&gt;Mp466: /* Tutorials */</title>
		<link rel="alternate" type="text/html" href="https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=AMBER&amp;diff=2610&amp;oldid=prev"/>
		<updated>2009-07-31T11:28:20Z</updated>

		<summary type="html">&lt;p&gt;&lt;span dir=&quot;auto&quot;&gt;&lt;span class=&quot;autocomment&quot;&gt;Tutorials&lt;/span&gt;&lt;/span&gt;&lt;/p&gt;
&lt;table style=&quot;background-color: #fff; color: #202122;&quot; data-mw=&quot;interface&quot;&gt;
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				&lt;tr class=&quot;diff-title&quot; lang=&quot;en&quot;&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #202122; text-align: center;&quot;&gt;← Older revision&lt;/td&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #202122; text-align: center;&quot;&gt;Revision as of 11:28, 31 July 2009&lt;/td&gt;
				&lt;/tr&gt;&lt;tr&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 11:&lt;/td&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 11:&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Generating parameters using RESP charges from GAMESS-US]]&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Generating parameters using RESP charges from GAMESS-US]]&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Simple scripts for LEaP to create topology and coordinate files]] &lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Simple scripts for LEaP to create topology and coordinate files]] &lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;a class=&quot;mw-diff-movedpara-left&quot; title=&quot;Paragraph was moved. Click to jump to new location.&quot; href=&quot;#movedpara_3_0_rhs&quot;&gt;&amp;#x26AB;&lt;/a&gt;&lt;/td&gt;
  &lt;td style=&quot;color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;&lt;a name=&quot;movedpara_1_0_lhs&quot;&gt;&lt;/a&gt;* [[Producing a PDB from a coordinates and topology file]] - using &#039;&#039;amdpdb&#039;&#039;&lt;/div&gt;&lt;/td&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-empty diff-side-added&quot;&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Preparing an AMBER topology file for a protein plus ligand system]] - step by step guide&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Preparing an AMBER topology file for a protein plus ligand system]] - step by step guide&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-empty diff-side-deleted&quot;&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;a class=&quot;mw-diff-movedpara-right&quot; title=&quot;Paragraph was moved. Click to jump to old location.&quot; href=&quot;#movedpara_1_0_lhs&quot;&gt;&amp;#x26AB;&lt;/a&gt;&lt;/td&gt;
  &lt;td style=&quot;color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;&lt;a name=&quot;movedpara_3_0_rhs&quot;&gt;&lt;/a&gt;* [[Producing a PDB from a coordinates and topology file]] - using &#039;&#039;amdpdb&#039;&#039;&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Running GMIN with MD move steps AMBER]]&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Running GMIN with MD move steps AMBER]]&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Running MD with AMBER]]&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Running MD with AMBER]]&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;</summary>
		<author><name>import&gt;Mp466</name></author>
	</entry>
	<entry>
		<id>https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=AMBER&amp;diff=2609&amp;oldid=prev</id>
		<title>import&gt;Csw34 at 18:54, 28 July 2009</title>
		<link rel="alternate" type="text/html" href="https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=AMBER&amp;diff=2609&amp;oldid=prev"/>
		<updated>2009-07-28T18:54:15Z</updated>

		<summary type="html">&lt;p&gt;&lt;/p&gt;
&lt;table style=&quot;background-color: #fff; color: #202122;&quot; data-mw=&quot;interface&quot;&gt;
				&lt;col class=&quot;diff-marker&quot; /&gt;
				&lt;col class=&quot;diff-content&quot; /&gt;
				&lt;col class=&quot;diff-marker&quot; /&gt;
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				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #202122; text-align: center;&quot;&gt;← Older revision&lt;/td&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #202122; text-align: center;&quot;&gt;Revision as of 18:54, 28 July 2009&lt;/td&gt;
				&lt;/tr&gt;&lt;tr&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 6:&lt;/td&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 6:&lt;/td&gt;
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&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;== Tutorials ==&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;== Tutorials ==&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;br /&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;br /&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot; data-marker=&quot;−&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Compiling AMBER Tools so you can start making input and analyzing output&lt;del style=&quot;font-weight: bold; text-decoration: none;&quot;&gt;!&lt;/del&gt;]]&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot; data-marker=&quot;+&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Compiling AMBER Tools so you can start making input and analyzing output]]&lt;ins style=&quot;font-weight: bold; text-decoration: none;&quot;&gt;!&lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [http://amber.scripps.edu/tutorials/ Ross Walker&#039;s AMBER9 tutorials] - recommended reading for &#039;&#039;&#039;ANYONE&#039;&#039;&#039; using AMBER!&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [http://amber.scripps.edu/tutorials/ Ross Walker&#039;s AMBER9 tutorials] - recommended reading for &#039;&#039;&#039;ANYONE&#039;&#039;&#039; using AMBER!&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Generating parameters using AMBER&#039;s built in General Forcefield (gaff)]]&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Generating parameters using AMBER&#039;s built in General Forcefield (gaff)]]&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;</summary>
		<author><name>import&gt;Csw34</name></author>
	</entry>
	<entry>
		<id>https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=AMBER&amp;diff=2608&amp;oldid=prev</id>
		<title>import&gt;Csw34 at 17:02, 28 July 2009</title>
		<link rel="alternate" type="text/html" href="https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=AMBER&amp;diff=2608&amp;oldid=prev"/>
		<updated>2009-07-28T17:02:52Z</updated>

		<summary type="html">&lt;p&gt;&lt;/p&gt;
&lt;table style=&quot;background-color: #fff; color: #202122;&quot; data-mw=&quot;interface&quot;&gt;
				&lt;col class=&quot;diff-marker&quot; /&gt;
				&lt;col class=&quot;diff-content&quot; /&gt;
				&lt;col class=&quot;diff-marker&quot; /&gt;
				&lt;col class=&quot;diff-content&quot; /&gt;
				&lt;tr class=&quot;diff-title&quot; lang=&quot;en&quot;&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #202122; text-align: center;&quot;&gt;← Older revision&lt;/td&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #202122; text-align: center;&quot;&gt;Revision as of 17:02, 28 July 2009&lt;/td&gt;
				&lt;/tr&gt;&lt;tr&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 1:&lt;/td&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 1:&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;[[Image:Amberpic.jpg|thumb|&quot;The bugs have magically disappeared!&quot;|200px|right]]&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;[[Image:Amberpic.jpg|thumb|&quot;The bugs have magically disappeared!&quot;|200px|right]]&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;[http://amber.scripps.edu/ &quot;AMBER&quot;] (Assisted Model Building with Energy Refinement) refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos. We mainly use the MM forcefields interfaced with other group software i.e. [[GMIN]] or [[OPTIM]]. The included programmes such as &#039;&#039;sander&#039;&#039; and &#039;&#039;antechamber&#039;&#039; are however, extremely useful in some circumstances! The full user manual for AMBER9 can be found in pdf format [http://amber.scripps.edu/doc9/amber9.pdf here].&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;[http://amber.scripps.edu/ &quot;AMBER&quot;] (Assisted Model Building with Energy Refinement) refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos. We mainly use the MM forcefields interfaced with other group software i.e. [[GMIN]] or [[OPTIM]]. The included programmes such as &#039;&#039;sander&#039;&#039; and &#039;&#039;antechamber&#039;&#039; are however, extremely useful in some circumstances! The full user manual for AMBER9 can be found in pdf format [http://amber.scripps.edu/doc9/amber9.pdf here].&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-empty diff-side-deleted&quot;&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot; data-marker=&quot;+&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;br /&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-empty diff-side-deleted&quot;&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot; data-marker=&quot;+&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;As of July 2009, the SVN repository also contains AMBER Tools, the stand alone suite of programs that generate AMBER input files and allow you to analyse output. You can find a manual within the repository. Look in AMBERTOOLS/doc.&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;br /&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;br /&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;== Tutorials ==&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;== Tutorials ==&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;br /&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;br /&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-empty diff-side-deleted&quot;&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot; data-marker=&quot;+&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Compiling AMBER Tools so you can start making input and analyzing output!]]&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [http://amber.scripps.edu/tutorials/ Ross Walker&#039;s AMBER9 tutorials] - recommended reading for &#039;&#039;&#039;ANYONE&#039;&#039;&#039; using AMBER!&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [http://amber.scripps.edu/tutorials/ Ross Walker&#039;s AMBER9 tutorials] - recommended reading for &#039;&#039;&#039;ANYONE&#039;&#039;&#039; using AMBER!&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Generating parameters using AMBER&#039;s built in General Forcefield (gaff)]]&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Generating parameters using AMBER&#039;s built in General Forcefield (gaff)]]&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;</summary>
		<author><name>import&gt;Csw34</name></author>
	</entry>
	<entry>
		<id>https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=AMBER&amp;diff=2607&amp;oldid=prev</id>
		<title>import&gt;Mp466: /* Tutorials */</title>
		<link rel="alternate" type="text/html" href="https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=AMBER&amp;diff=2607&amp;oldid=prev"/>
		<updated>2009-07-28T12:52:02Z</updated>

		<summary type="html">&lt;p&gt;&lt;span dir=&quot;auto&quot;&gt;&lt;span class=&quot;autocomment&quot;&gt;Tutorials&lt;/span&gt;&lt;/span&gt;&lt;/p&gt;
&lt;table style=&quot;background-color: #fff; color: #202122;&quot; data-mw=&quot;interface&quot;&gt;
				&lt;col class=&quot;diff-marker&quot; /&gt;
				&lt;col class=&quot;diff-content&quot; /&gt;
				&lt;col class=&quot;diff-marker&quot; /&gt;
				&lt;col class=&quot;diff-content&quot; /&gt;
				&lt;tr class=&quot;diff-title&quot; lang=&quot;en&quot;&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #202122; text-align: center;&quot;&gt;← Older revision&lt;/td&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #202122; text-align: center;&quot;&gt;Revision as of 12:52, 28 July 2009&lt;/td&gt;
				&lt;/tr&gt;&lt;tr&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 10:&lt;/td&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 10:&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Producing a PDB from a coordinates and topology file]] - using &#039;&#039;amdpdb&#039;&#039;&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Producing a PDB from a coordinates and topology file]] - using &#039;&#039;amdpdb&#039;&#039;&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Preparing an AMBER topology file for a protein plus ligand system]] - step by step guide&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Preparing an AMBER topology file for a protein plus ligand system]] - step by step guide&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-empty diff-side-deleted&quot;&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot; data-marker=&quot;+&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Running GMIN with MD move steps AMBER]]&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Running MD with AMBER]]&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Running MD with AMBER]]&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[REMD with AMBER]]&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[REMD with AMBER]]&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;</summary>
		<author><name>import&gt;Mp466</name></author>
	</entry>
	<entry>
		<id>https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=AMBER&amp;diff=2606&amp;oldid=prev</id>
		<title>import&gt;Bs360 at 17:48, 11 July 2008</title>
		<link rel="alternate" type="text/html" href="https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=AMBER&amp;diff=2606&amp;oldid=prev"/>
		<updated>2008-07-11T17:48:04Z</updated>

		<summary type="html">&lt;p&gt;&lt;/p&gt;
&lt;table style=&quot;background-color: #fff; color: #202122;&quot; data-mw=&quot;interface&quot;&gt;
				&lt;col class=&quot;diff-marker&quot; /&gt;
				&lt;col class=&quot;diff-content&quot; /&gt;
				&lt;col class=&quot;diff-marker&quot; /&gt;
				&lt;col class=&quot;diff-content&quot; /&gt;
				&lt;tr class=&quot;diff-title&quot; lang=&quot;en&quot;&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #202122; text-align: center;&quot;&gt;← Older revision&lt;/td&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #202122; text-align: center;&quot;&gt;Revision as of 17:48, 11 July 2008&lt;/td&gt;
				&lt;/tr&gt;&lt;tr&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 11:&lt;/td&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 11:&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Preparing an AMBER topology file for a protein plus ligand system]] - step by step guide&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Preparing an AMBER topology file for a protein plus ligand system]] - step by step guide&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Running MD with AMBER]]&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Running MD with AMBER]]&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-empty diff-side-deleted&quot;&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot; data-marker=&quot;+&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[REMD with AMBER]]&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;</summary>
		<author><name>import&gt;Bs360</name></author>
	</entry>
	<entry>
		<id>https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=AMBER&amp;diff=2605&amp;oldid=prev</id>
		<title>import&gt;Csw34 at 16:59, 20 May 2008</title>
		<link rel="alternate" type="text/html" href="https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=AMBER&amp;diff=2605&amp;oldid=prev"/>
		<updated>2008-05-20T16:59:17Z</updated>

		<summary type="html">&lt;p&gt;&lt;/p&gt;
&lt;table style=&quot;background-color: #fff; color: #202122;&quot; data-mw=&quot;interface&quot;&gt;
				&lt;col class=&quot;diff-marker&quot; /&gt;
				&lt;col class=&quot;diff-content&quot; /&gt;
				&lt;col class=&quot;diff-marker&quot; /&gt;
				&lt;col class=&quot;diff-content&quot; /&gt;
				&lt;tr class=&quot;diff-title&quot; lang=&quot;en&quot;&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #202122; text-align: center;&quot;&gt;← Older revision&lt;/td&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #202122; text-align: center;&quot;&gt;Revision as of 16:59, 20 May 2008&lt;/td&gt;
				&lt;/tr&gt;&lt;tr&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 7:&lt;/td&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 7:&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Generating parameters using AMBER&#039;s built in General Forcefield (gaff)]]&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Generating parameters using AMBER&#039;s built in General Forcefield (gaff)]]&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Generating parameters using RESP charges from GAMESS-US]]&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Generating parameters using RESP charges from GAMESS-US]]&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot; data-marker=&quot;−&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Simple scripts for LEaP to create topology and coordinate files]] &lt;del style=&quot;font-weight: bold; text-decoration: none;&quot;&gt;- using &#039;&#039;ampdb&#039;&#039;&lt;/del&gt;&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot; data-marker=&quot;+&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Simple scripts for LEaP to create topology and coordinate files]] &lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot; data-marker=&quot;−&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Producing a PDB from a coordinates and topology file]]&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot; data-marker=&quot;+&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Producing a PDB from a coordinates and topology file]]&lt;ins style=&quot;font-weight: bold; text-decoration: none;&quot;&gt; - using &#039;&#039;amdpdb&#039;&#039;&lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Preparing an AMBER topology file for a protein plus ligand system]] - step by step guide&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Preparing an AMBER topology file for a protein plus ligand system]] - step by step guide&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Running MD with AMBER]]&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Running MD with AMBER]]&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;</summary>
		<author><name>import&gt;Csw34</name></author>
	</entry>
	<entry>
		<id>https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=AMBER&amp;diff=2604&amp;oldid=prev</id>
		<title>import&gt;Csw34 at 16:58, 20 May 2008</title>
		<link rel="alternate" type="text/html" href="https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=AMBER&amp;diff=2604&amp;oldid=prev"/>
		<updated>2008-05-20T16:58:51Z</updated>

		<summary type="html">&lt;p&gt;&lt;/p&gt;
&lt;table style=&quot;background-color: #fff; color: #202122;&quot; data-mw=&quot;interface&quot;&gt;
				&lt;col class=&quot;diff-marker&quot; /&gt;
				&lt;col class=&quot;diff-content&quot; /&gt;
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				&lt;col class=&quot;diff-content&quot; /&gt;
				&lt;tr class=&quot;diff-title&quot; lang=&quot;en&quot;&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #202122; text-align: center;&quot;&gt;← Older revision&lt;/td&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #202122; text-align: center;&quot;&gt;Revision as of 16:58, 20 May 2008&lt;/td&gt;
				&lt;/tr&gt;&lt;tr&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 7:&lt;/td&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 7:&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Generating parameters using AMBER&#039;s built in General Forcefield (gaff)]]&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Generating parameters using AMBER&#039;s built in General Forcefield (gaff)]]&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Generating parameters using RESP charges from GAMESS-US]]&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Generating parameters using RESP charges from GAMESS-US]]&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot; data-marker=&quot;−&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Simple scripts for LEaP to create topology and coordinate files]]&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot; data-marker=&quot;+&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Simple scripts for LEaP to create topology and coordinate files]]&lt;ins style=&quot;font-weight: bold; text-decoration: none;&quot;&gt; - using &#039;&#039;ampdb&#039;&#039;&lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Producing a PDB from a coordinates and topology file]]&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Producing a PDB from a coordinates and topology file]]&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Preparing an AMBER topology file for a protein plus ligand system]] - step by step guide&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Preparing an AMBER topology file for a protein plus ligand system]] - step by step guide&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;</summary>
		<author><name>import&gt;Csw34</name></author>
	</entry>
	<entry>
		<id>https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=AMBER&amp;diff=2603&amp;oldid=prev</id>
		<title>import&gt;Csw34 at 15:17, 20 May 2008</title>
		<link rel="alternate" type="text/html" href="https://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=AMBER&amp;diff=2603&amp;oldid=prev"/>
		<updated>2008-05-20T15:17:09Z</updated>

		<summary type="html">&lt;p&gt;&lt;/p&gt;
&lt;table style=&quot;background-color: #fff; color: #202122;&quot; data-mw=&quot;interface&quot;&gt;
				&lt;col class=&quot;diff-marker&quot; /&gt;
				&lt;col class=&quot;diff-content&quot; /&gt;
				&lt;col class=&quot;diff-marker&quot; /&gt;
				&lt;col class=&quot;diff-content&quot; /&gt;
				&lt;tr class=&quot;diff-title&quot; lang=&quot;en&quot;&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #202122; text-align: center;&quot;&gt;← Older revision&lt;/td&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #202122; text-align: center;&quot;&gt;Revision as of 15:17, 20 May 2008&lt;/td&gt;
				&lt;/tr&gt;&lt;tr&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 8:&lt;/td&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 8:&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Generating parameters using RESP charges from GAMESS-US]]&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Generating parameters using RESP charges from GAMESS-US]]&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Simple scripts for LEaP to create topology and coordinate files]]&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Simple scripts for LEaP to create topology and coordinate files]]&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td colspan=&quot;2&quot; class=&quot;diff-empty diff-side-deleted&quot;&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot; data-marker=&quot;+&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Producing a PDB from a coordinates and topology file]]&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Preparing an AMBER topology file for a protein plus ligand system]] - step by step guide&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Preparing an AMBER topology file for a protein plus ligand system]] - step by step guide&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;tr&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Running MD with AMBER]]&lt;/div&gt;&lt;/td&gt;
  &lt;td class=&quot;diff-marker&quot;&gt;&lt;/td&gt;
  &lt;td style=&quot;background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* [[Running MD with AMBER]]&lt;/div&gt;&lt;/td&gt;
&lt;/tr&gt;
&lt;/table&gt;</summary>
		<author><name>import&gt;Csw34</name></author>
	</entry>
</feed>