Re: combine pdb files

From: Jeffrey J. Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Sun Jun 03 2007 - 10:11:49 CDT

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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