[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:
>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:
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.
>gmx-users mailing list
>gmx-users at gromacs.org
>Please don't post (un)subscribe requests to the list. Use the
>www interface or send it to gmx-users-request at gromacs.org.
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
More information about the gromacs.org_gmx-users