From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sun Jun 03 2007 - 10:33:02 CDT
Just to add to that, if you already have created separate psf files, you can
do it even more easily:
resetpsf
readpsf protein.psf
coordpdb protein.pdb
readpsf sugar.psf
coordpdb sugar.pdb
writepsf ___.psf
writepdb ___.pdb
-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Jeffrey J. Potoff
Sent: Sunday, June 03, 2007 10:12 AM
To: Richard Casey
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: combine pdb files
On Sun, 3 Jun 2007, Richard Casey wrote:
> Hello,
>
> I have two separate PDB files, call them protein.pdb and sugar.pdb, that
> I need to combine into a single PDB file before running NAMD
> simulations. Does anyone know how to combine PDB files?
The easiest way is to write a tcl script to do this. Save the
following in a file (build.tcl, for example), make executable and do
./build.tcl at the command prompt
===================================================================
psfgen <<ENDMOL
topology top_all27_prot_lipid.inp
# build protein
segment PROT {
pdb protein.pdb
first none
last none
}
# first none, last none req'd to prevent auto termination of residues.
#build sugar segment
segment SUG {
auto none
pdb sugar.pdb
}
#Read coordinates
coordpdb protein.pdb PROT
coordpdb sugar.pdb SUG
#write PSF and PDB files
writepsf protein_start.psf
writepdb protein_start.pdb
======================================================================
Jeffrey J. Potoff jpotoff_at_chem1.eng.wayne.edu
Associate Professor Wayne State University
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr Phone:(313)577-9357
Detroit, MI 48202 Fax: (313)577-3810
http://potoff1.eng.wayne.edu
======================================================================
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