[gmx-users] using charmm force fields with gmx v3.3

Mu Yuguang (Dr) YGMu at ntu.edu.sg
Sat Dec 24 09:22:10 CET 2005

This charm 27 force field was used with gromacs 3.1 and 3.2 . I did not use it with gromacs 3.3.

I think maybe there are some differences between 3.1, 3.2 and 3.3 in creating terminal groups.

Anyway as I suggested in the readme file that you can prepare the pdb file with original charm program including add hydrogen atoms, terminals, et.al. Then just use pdb2gmx to create top file with -ter switch answered by none.


Dr. Yuguang Mu
Division of Computational and Structrual Biology
School of Biological Sciences
Nanyang Technological University
Singapore 637820
Tel: 0065-63162885
Mail: ygmu at ntu.edu.sg

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of leafyoung81-group at yahoo.com
Sent: 2005年12月24日 14:28
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] using charmm force fields with gmx v3.3


This CHARM27 FF is supposed to be used by Gromacs 3.3. You may check ffgmx2-c.tdb from different versions of gromacs and change the file format accordingly.

Yang Ye

----- Original Message ----
From: dimka <newyorkdimka at gmail.com>
To: gmx-users at gromacs.org
Sent: Saturday, December 24, 2005 7:37:23 AM
Subject: [gmx-users] using charmm force fields with gmx v3.3

Hello, I've downloaded charmm27 force fields (from http://www.gromacs.org/topologies/force_fields.php) and followed installation instructions.
When I try to generate topology and structure file I'm getting the following using Charmm27 ff I'm g etting the following error:

Opening library file /usr/gmx/share/gromacs/top/ffcharmm-n.tdb
Program pdb2gmx, VERSION 3.3
Source code file: ter_db.c, line: 85

Fatal error:
Reading Termini Database: expected 3 items of atom data in stead of 1 on line
       N &nbs p;    NH3        14.0027    -0.3000

I spent some time trying looking at the ffcharmm-n.tdb but i cannot figure out its format.
Can anyone point me to the description of the file format?


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