[gmx-users] Making pdb files

Raymond C. Fort Jr. rcfort at maine.edu
Tue Aug 3 21:58:20 CEST 2004

At 03:46 PM 8/3/2004 -0400, you wrote:
>Hi Guys!
>I need to make a pdb file for a peptide we are using.  I know that I can 
>create one in a program like chem3d but when I use that file it doesn't 
>work in gromacs.  I am creating the pdb on a mac and using gromacs on a 
>linux box.  I have tried doing some light editting to make it work but the 
>backbone doesn't even appear to be connected.  What is everyone else doing 
>to make pdb files?  Thanks!

We're using a program called B, from the Case group at Scripps: 

It's free.

A commercial program that writes almost standard pdb files is PCModel, from 
Serena Software: http://www.serenasoft.com

Academic pricing is offered, and it has the advantage that is has the best 
molecular mechanics forcefield going.


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Professor Ray Fort Jr.                  rcfort at maine.edu
Department of Chemistry         chemistry.umeche.maine.edu/fort.html
University of Maine                     Voice: (207)-581-1180
Orono, ME 04469                 FAX: (207)-581-1191

Computer modeling of organic and biomolecules; chemistry of lignin
and cellulose   

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