Converting between '.crd' and '.pdb' - Revision history

import>Jmc49 at 16:04, 19 August 2009

2009-08-19T16:04:59Z

← Older revision		Revision as of 16:04, 19 August 2009
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	'''NOTE:''' You need only specify the FREE keyword when '''READING''' a crd format file.		'''NOTE:''' You need only specify the FREE keyword when '''READING''' a crd format file.

			[[If you need to change the number of atoms (e.g. making a united-atom charmm19 .crd file, or if atoms are missing)]]

	Once you've got your input file set up, you run it through CHARMM like this:		Once you've got your input file set up, you run it through CHARMM like this:

import>Csw34 at 08:04, 24 July 2008

2008-07-24T08:04:12Z

← Older revision		Revision as of 08:04, 24 July 2008
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	<pre>		<pre>
	! Read in the ~~crd~~ format input file into the COOR array		! Read in the pdb format input file into the COOR array

	OPEN UNIT 20 NAME input.pdb READ CARD		OPEN UNIT 20 NAME input.pdb READ CARD
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	IC BUILD		IC BUILD

	! Write the COOR array out in ~~pdb~~ format		! Write the COOR array out in crd format

	OPEN UNIT 20 NAME input.crd WRITE CARD		OPEN UNIT 20 NAME input.crd WRITE CARD
Line 69:		Line 69:
	CLOSE UNIT 20		CLOSE UNIT 20
	</pre>		</pre>

			'''NOTE:''' You need only specify the FREE keyword when '''READING''' a crd format file.

	Once you've got your input file set up, you run it through CHARMM like this:		Once you've got your input file set up, you run it through CHARMM like this:

import>Csw34 at 21:52, 23 July 2008

2008-07-23T21:52:00Z

← Older revision		Revision as of 21:52, 23 July 2008
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	</pre>		</pre>

	You'll see if CHARMM didn't exit properly by the big skull in the output!~~</pre>~~		You'll see if CHARMM didn't exit properly by the big skull in the output! Here is a CARD file for the met-enk peptide so you can have a play!

			[[Media:Input.crd.txt \| input.crd]]

import>Csw34 at 21:46, 23 July 2008

2008-07-23T21:46:33Z

← Older revision		Revision as of 21:46, 23 July 2008
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	<pre>		<pre>
	! CHARMM printing and error tolerence		! CHARMM printing and error tolerence

	PRNLev 1		PRNLev 1
	BOMLev -5		BOMLev -5

import>Csw34 at 21:46, 23 July 2008

2008-07-23T21:46:05Z

← Older revision		Revision as of 21:46, 23 July 2008
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	<pre>		<pre>
	charmm < crd2pdb.inp		charmm < crd2pdb.inp
	</~~pdb~~>		</pre>

	You'll see if CHARMM didn't exit properly by the big skull in the output!</pre>		You'll see if CHARMM didn't exit properly by the big skull in the output!</pre>

import>Csw34 at 21:45, 23 July 2008

2008-07-23T21:45:36Z

← Older revision		Revision as of 21:45, 23 July 2008
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	You can actually convert between '.xyz', '.pdb' and '.crd' formats using ''awk'' and other shell commands. There is more info on the [[conversion between different data file formats]] page. Another way of doing it is using CHARMM to read in your structure in one format and then specifying that you would like to save it in a different format. The advantage of using CHARMM for this is that you know the output structure will be readable by CHARMM!		You can actually convert between '.xyz', '.pdb' and '.crd' formats using ''awk'' and other shell commands. There is more info on the [[conversion between different data file formats]] page. Another way of doing it is using CHARMM to read in your structure in one format and then specifying that you would like to save it in a different format. The advantage of using CHARMM for this is that you know the output structure will be readable by CHARMM!

			As an example, here is a CHARMM input file which will convert a set of cooridinates in CARD (crd) format into a pdb. The different parts of the input file are described in more detail on the [[CHARMM]] page.

			<pre>
			! CHARMM printing and error tolerence
			PRNLev 1
			BOMLev -5

			! Read standard topology and parameter files

			OPEN READ CARD UNIT 1 NAME "/home/csw34/svn/CHARMM31/toppar/toph19_eef1_perm.inp"
			READ RTF CARD UNIT 1
			CLOSE UNIT 1

			OPEN READ CARD UNIT 2 NAME "/home/csw34/svn/CHARMM31/toppar/param19_eef1_perm.inp"
			READ PARAMETER CARD UNIT 2
			CLOSE UNIT 2

			! Generate the PSF for met-enk

			READ SEQUence CARD
			*
			5
			TYR GLY GLY PHE MET
			GENErate FIRS NTER LAST CTER SETUp

			! Read in the crd format input file into the COOR array

			OPEN UNIT 20 NAME input.crd READ CARD
			READ COOR UNIT 20 CARD FREE
			CLOSE UNIT 20

			! Fill and setup the internal coordinate tables

			IC FILL PRESERVE
			IC PARAMETERS
			IC PURGE
			IC BUILD

			! Write the COOR array out in pdb format

			OPEN UNIT 20 NAME input.pdb WRITE CARD
			WRITE COOR UNIT 20 PDB
			CLOSE UNIT 20
			</pre>

			If you wanted to go the other way, from pdb to crd, the bottom of the input file should be:

			<pre>
			! Read in the crd format input file into the COOR array

			OPEN UNIT 20 NAME input.pdb READ CARD
			READ COOR UNIT 20 PDB
			CLOSE UNIT 20

			! Fill and setup the internal coordinate tables

			IC FILL PRESERVE
			IC PARAMETERS
			IC PURGE
			IC BUILD

			! Write the COOR array out in pdb format

			OPEN UNIT 20 NAME input.crd WRITE CARD
			WRITE COOR UNIT 20 CARD
			CLOSE UNIT 20
			</pre>

			Once you've got your input file set up, you run it through CHARMM like this:

			<pre>
			charmm < crd2pdb.inp
			</pdb>

			You'll see if CHARMM didn't exit properly by the big skull in the output!</pre>

import>Csw34 at 20:00, 30 April 2008

2008-04-30T20:00:32Z

← Older revision		Revision as of 20:00, 30 April 2008
Line 1:		Line 1:
	You can actually convert between '.xyz', '.pdb' and '.crd' formats using ''awk'' and other shell commands. There is more info on the [[conversion between different data file formats]] page. Another way of doing it is using CHARMM to read in your structure in one format and then specifying that you would like to save it in a different format.		You can actually convert between '.xyz', '.pdb' and '.crd' formats using ''awk'' and other shell commands. There is more info on the [[conversion between different data file formats]] page. Another way of doing it is using CHARMM to read in your structure in one format and then specifying that you would like to save it in a different format. The advantage of using CHARMM for this is that you know the output structure will be readable by CHARMM!

import>Csw34 at 18:49, 30 April 2008

2008-04-30T18:49:31Z

New page

You can actually convert between '.xyz', '.pdb' and '.crd' formats using ''awk'' and other shell commands. There is more info on the [[conversion between different data file formats]] page. Another way of doing it is using CHARMM to read in your structure in one format and then specifying that you would like to save it in a different format.