Setting up (CHARMM) - Revision history

import>Csw34 at 14:52, 8 February 2012

2012-02-08T14:52:50Z

← Older revision		Revision as of 14:52, 8 February 2012
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	You can download the PDB we're using as the starting point for this tutorial		You can download the PDB we're using as the starting point for this tutorial
	[http://www-wales.ch.cam.ac.uk/chris/~~COPTIM_tutorial~~/metenk.pdb here].		[http://www-wales.ch.cam.ac.uk/chris/metenk_tutorial/metenk.pdb here].

	=== Converting a PDB into CHARMM .crd (CARD) format ===		=== Converting a PDB into CHARMM .crd (CARD) format ===
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	</pre>		</pre>
	If you get a skull and crossbones, ask someone for help! If you wanted to do this for your own system, you would of course need to also modify the ''PSF'' section appropriately. You should now have a ''metenk.crd'' file, identical to		If you get a skull and crossbones, ask someone for help! If you wanted to do this for your own system, you would of course need to also modify the ''PSF'' section appropriately. You should now have a ''metenk.crd'' file, identical to
	[http://www-wales.ch.cam.ac.uk/chris/~~COPTIM_tutorial~~/metenk.~~pdb~~ this] one.		[http://www-wales.ch.cam.ac.uk/chris/metenk_tutorial/metenk.crd this] one.

	That's it! We're pretty much good to go. As we're going to be using OPTIM later though, this is a good time to make a '''perm.allow''' file for your system...		That's it! We're pretty much good to go. As we're going to be using OPTIM later though, this is a good time to make a '''perm.allow''' file for your system...
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	</pre>		</pre>

	Your ''metenk_perm.pdb'' file should be identical to [http://www-wales.ch.cam.ac.uk/chris/~~COPTIM_tutorial~~/metenk_perm.pdb this] one. Now that we have the altered PDB, we can run a script to generate the ''perm.allow'' file for us:		Your ''metenk_perm.pdb'' file should be identical to [http://www-wales.ch.cam.ac.uk/chris/metenk_tutorial/metenk_perm.pdb this] one. Now that we have the altered PDB, we can run a script to generate the ''perm.allow'' file for us:
	<pre>		<pre>
	~/svn/SCRIPTS/make_perm.allow/perm-pdb-ua.py metenk_perm.pdb CHARMM		~/svn/SCRIPTS/make_perm.allow/perm-pdb-ua.py metenk_perm.pdb CHARMM

import>Csw34: /* Making a perm.allow file for later */

2012-02-07T17:28:59Z

Making a perm.allow file for later

← Older revision		Revision as of 17:28, 7 February 2012
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	'''AS OF 07/02/2012 THIS STEP DOES NOT WORK AS THE SCRIPT ONLY SUPPORTS AMBER - THIS WILL BE CORRECTED SOON! FOR NOW, JUST TAKE A COPY OF THE BELOW perm.allow FILE :)'''		'''AS OF 07/02/2012 THIS STEP DOES NOT WORK AS THE SCRIPT ONLY SUPPORTS AMBER - THIS WILL BE CORRECTED SOON! FOR NOW, JUST TAKE A COPY OF THE BELOW perm.allow FILE :)'''

	You should get a perm.allow file like this:		You should get a ''perm.allow'' file like this:
	<pre>		<pre>
	4		4

import>Csw34: /* Making a perm.allow file for later */

2012-02-07T17:28:42Z

Making a perm.allow file for later

← Older revision		Revision as of 17:28, 7 February 2012
Line 115:		Line 115:
	</pre>		</pre>

	Your metenk_perm.pdb file should be identical to [http://www-wales.ch.cam.ac.uk/chris/COPTIM_tutorial/metenk_perm.pdb this] one. Now that we have the altered PDB, we can run a script to generate the ''perm.allow'' file for us:		Your ''metenk_perm.pdb'' file should be identical to [http://www-wales.ch.cam.ac.uk/chris/COPTIM_tutorial/metenk_perm.pdb this] one. Now that we have the altered PDB, we can run a script to generate the ''perm.allow'' file for us:
	<pre>		<pre>
	~/svn/SCRIPTS/make_perm.allow/perm-pdb-ua.py metenk_perm.pdb CHARMM		~/svn/SCRIPTS/make_perm.allow/perm-pdb-ua.py metenk_perm.pdb CHARMM

import>Csw34: /* Making a perm.allow file for later */

2012-02-07T17:28:24Z

Making a perm.allow file for later

← Older revision		Revision as of 17:28, 7 February 2012
Line 115:		Line 115:
	</pre>		</pre>

	Now that we have the altered PDB, we can run a script to generate the ''perm.allow'' file for us:		Your metenk_perm.pdb file should be identical to [http://www-wales.ch.cam.ac.uk/chris/COPTIM_tutorial/metenk_perm.pdb this] one. Now that we have the altered PDB, we can run a script to generate the ''perm.allow'' file for us:
	<pre>		<pre>
	~/svn/SCRIPTS/make_perm.allow/perm-pdb-ua.py metenk_perm.pdb CHARMM		~/svn/SCRIPTS/make_perm.allow/perm-pdb-ua.py metenk_perm.pdb CHARMM
	</pre>		</pre>

	Your metenk_perm.pdb file should be identical to [http://www-wales.ch.cam.ac.uk/chris/COPTIM_tutorial/metenk_perm.pdb this] one.

	'''AS OF 07/02/2012 THIS STEP DOES NOT WORK AS THE SCRIPT ONLY SUPPORTS AMBER - THIS WILL BE CORRECTED SOON! FOR NOW, JUST TAKE A COPY OF THE BELOW perm.allow FILE :)'''		'''AS OF 07/02/2012 THIS STEP DOES NOT WORK AS THE SCRIPT ONLY SUPPORTS AMBER - THIS WILL BE CORRECTED SOON! FOR NOW, JUST TAKE A COPY OF THE BELOW perm.allow FILE :)'''

import>Csw34: /* Making a perm.allow file for later */

2012-02-07T17:24:21Z

Making a perm.allow file for later

← Older revision		Revision as of 17:24, 7 February 2012
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	~/svn/SCRIPTS/make_perm.allow/perm-pdb-ua.py metenk_perm.pdb CHARMM		~/svn/SCRIPTS/make_perm.allow/perm-pdb-ua.py metenk_perm.pdb CHARMM
	</pre>		</pre>

			Your metenk_perm.pdb file should be identical to [http://www-wales.ch.cam.ac.uk/chris/COPTIM_tutorial/metenk_perm.pdb this] one.

	'''AS OF 07/02/2012 THIS STEP DOES NOT WORK AS THE SCRIPT ONLY SUPPORTS AMBER - THIS WILL BE CORRECTED SOON! FOR NOW, JUST TAKE A COPY OF THE BELOW perm.allow FILE :)'''		'''AS OF 07/02/2012 THIS STEP DOES NOT WORK AS THE SCRIPT ONLY SUPPORTS AMBER - THIS WILL BE CORRECTED SOON! FOR NOW, JUST TAKE A COPY OF THE BELOW perm.allow FILE :)'''

import>Csw34: /* Converting a PDB into CHARMM .crd (CARD) format */

2012-02-07T17:19:41Z

Converting a PDB into CHARMM .crd (CARD) format

← Older revision		Revision as of 17:19, 7 February 2012
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	If you get a skull and crossbones, ask someone for help! If you wanted to do this for your own system, you would of course need to also modify the ''PSF'' section appropriately. You should now have a ''metenk.crd'' file, identical to		If you get a skull and crossbones, ask someone for help! If you wanted to do this for your own system, you would of course need to also modify the ''PSF'' section appropriately. You should now have a ''metenk.crd'' file, identical to
	[http://www-wales.ch.cam.ac.uk/chris/COPTIM_tutorial/metenk.pdb this] one.		[http://www-wales.ch.cam.ac.uk/chris/COPTIM_tutorial/metenk.pdb this] one.

			That's it! We're pretty much good to go. As we're going to be using OPTIM later though, this is a good time to make a '''perm.allow''' file for your system...

	=== Making a perm.allow file for later ===		=== Making a perm.allow file for later ===

import>Csw34 at 17:18, 7 February 2012

2012-02-07T17:18:35Z

← Older revision		Revision as of 17:18, 7 February 2012
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	</pre>		</pre>

	'''AS OF 07/02/2012 THIS STEP DOES NOT WORK AS THE SCRIPT ONLY SUPPORTS AMBER - THIS WILL BE CORRECTED SOON!'''		'''AS OF 07/02/2012 THIS STEP DOES NOT WORK AS THE SCRIPT ONLY SUPPORTS AMBER - THIS WILL BE CORRECTED SOON! FOR NOW, JUST TAKE A COPY OF THE BELOW perm.allow FILE :)'''

	You should get a perm.allow file like this:		You should get a perm.allow file like this:
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	47 48		47 48
	</pre>		</pre>
	The first line specifies that there are four permutable groups, in this case, NH3 of NTYR, atoms in the ring of NTYR, atoms in the ring of PHE and the COO- of CMET. Taking the first two as examples for the NH3 of NTYR, '3 0' says that there are three identical atoms, and that no other triples need move with them. In this case, these atoms are 1, 2 and 4. For the atoms in the ring of NTYR, two pairs of C atoms are identical (there is a mirror plane down the middle of the ring). If you were to flip one of these pairs however, you must also flip the other as the whole ring has been rotated. This is how we get to '2 1', with the 2 designating a pair, and the 1 that there is a second pair that must also be permuted at the same time. The four atoms below are the two pairs, 8 and 10, 9 and 11.		The first line specifies that there are four permutable groups, in this case, NH3 of NTYR, atoms in the ring of NTYR, atoms in the ring of PHE and the COO- of CMET.
			<pre>
			3 0
			1 2 4
			</pre>
			Taking the first two as examples for the NH3 of NTYR, '3 0' says that there are three identical atoms, and that no other triples need move with them. In this case, these atoms are 1, 2 and 4.
			<pre>
			2 1
			8 10 9 11
			</pre>
			For the atoms in the ring of NTYR, two pairs of C atoms are identical (there is a mirror plane down the middle of the ring). If you were to flip one of these pairs however, you must also flip the other as the whole ring has been rotated. This is how we get to '2 1', with the 2 designating a pair, and the 1 that there is a second pair that must also be permuted at the same time. The four atoms below are the two pairs, 8 and 10, 9 and 11.

import>Csw34: /* Making a perm.allow file for later */

2012-02-07T17:17:02Z

Making a perm.allow file for later

← Older revision		Revision as of 17:17, 7 February 2012
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	sed 's/TYR 1/NTYR 1/' metenk.pdb \| sed 's/MET 5/CMET 5/' > metenk_perm.pdb		sed 's/TYR 1/NTYR 1/' metenk.pdb \| sed 's/MET 5/CMET 5/' > metenk_perm.pdb
	</pre>		</pre>

			Now that we have the altered PDB, we can run a script to generate the ''perm.allow'' file for us:
			<pre>
			~/svn/SCRIPTS/make_perm.allow/perm-pdb-ua.py metenk_perm.pdb CHARMM
			</pre>

			'''AS OF 07/02/2012 THIS STEP DOES NOT WORK AS THE SCRIPT ONLY SUPPORTS AMBER - THIS WILL BE CORRECTED SOON!'''

			You should get a perm.allow file like this:
			<pre>
			4
			3 0
			1 2 4
			2 1
			8 10 9 11
			2 1
			32 33 34 35
			2 0
			47 48
			</pre>
			The first line specifies that there are four permutable groups, in this case, NH3 of NTYR, atoms in the ring of NTYR, atoms in the ring of PHE and the COO- of CMET. Taking the first two as examples for the NH3 of NTYR, '3 0' says that there are three identical atoms, and that no other triples need move with them. In this case, these atoms are 1, 2 and 4. For the atoms in the ring of NTYR, two pairs of C atoms are identical (there is a mirror plane down the middle of the ring). If you were to flip one of these pairs however, you must also flip the other as the whole ring has been rotated. This is how we get to '2 1', with the 2 designating a pair, and the 1 that there is a second pair that must also be permuted at the same time. The four atoms below are the two pairs, 8 and 10, 9 and 11.

import>Csw34: /* Making a perm.allow file for later */

2012-02-07T17:08:01Z

Making a perm.allow file for later

← Older revision		Revision as of 17:08, 7 February 2012
Line 85:		Line 85:

	=== Making a perm.allow file for later ===		=== Making a perm.allow file for later ===

			The perm.allow file specifies which groups can be permuted when aligning endpoints of paths. For example, it ensures that all three H atoms of NH3 are treated as being the same, so NH3 rotation does not affect alignment, and two structures that differ only by a rotation of NH3 which permutes these atoms are correctly identified as being identical. To make a perm.allow file, we need a PDB that includes the termini being specified. This means we cannot use the original PDB without some modification. In this case, we need to change the N-terminal TYR residue to NTYR, and the C-terminal MET residue to CMET. We can easily do this in vi:

			First, we make a copy of the original PDB to modify, and open it in vi:
			<pre>
			cp metenk.pdb metenk_perm.pdb
			vi metenk_perm.pdb
			</pre>

			The fastest way to make the changes is using a 'find and replace' command. So, for the N-terminus:
			<pre>
			:%s/TYR 1/NTYR 1/
			</pre>
			and for the C-terminus:
			<pre>
			:%s/MET 5/CMET 5/
			</pre>

			You should see the changes have been made! We then save and exit:
			<pre>
			:wq
			</pre>

			'''ASIDE: we could also have done this using sed and regular expressions, like this:'''
			<pre>
			sed 's/TYR 1/NTYR 1/' metenk.pdb \| sed 's/MET 5/CMET 5/' > metenk_perm.pdb
			</pre>

import>Csw34: /* Converting a PDB into CHARMM .crd (CARD) format */

2012-02-07T13:46:40Z

Converting a PDB into CHARMM .crd (CARD) format

@@ Line 60: / Line 60: @@
 Assuming you have CHARMM in your path, and that you are in the directory containing ''metenk.pdb'', you can run this simply using:
 <pre>
 charmm < pdb2crd.inp
 </pre>
 [http://www-wales.ch.cam.ac.uk/chris/COPTIM_tutorial/metenk.pdb this] one.