[gmx-users] files missing

Rahul Karyappa r.karyappa at ncl.res.in
Thu Aug 11 12:32:31 CEST 2005

Thank you for your kind reply. I am using gromacs version 3.2.

Actually sir, I am going to use it for synthetic polymers not for the
proteins etc. I had taken a test model of polyethylene (5 repeat units)
and when I tried to convert .PDB file to .GRO and .TOP using command
'pdb2gmx', it gave me error as follows:

Fatal error: Residue 'PE' not found in residue topology database

This was the case with all the test model polymers I tried.

I am stuck right now. Please help me out. Thanking you.

Rahul Karyappa

NCL, Pune


-- Original Message --
From: David <spoel at xray.bmc.uu.se>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Thu, 11 Aug 2005 09:08:23 +0200
Subject: Re: [gmx-users] files missing
On Thu, 2005-08-11 at 10:18 +0530, Rahul Karyappa wrote:
> Dear all,
> I ran x2top command to get .top file from .gro. But it gave me error
> for all the forcefields I used. The error was as follows:
> Fatal error: Library file ffG43a1.n2t not found in current dir nor in
> default directories.
> Also when I used other forcefields it gave me same errors but the file
> names were different i.e. ffG43b1.n2t, ffG43a2.n2t, ffoplsaa.n2t and
> ffgmx2.n2t.
> Please tell me where I can get these files. I have searched for these
> files on my pc (/usr/local/gromacs/share/top) but these are not there.
> Waiting for your kind reply.
> Rahul Karyappa
> NCL, Pune
> India
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Which gromacs version?
I'm attaching the ffgmx version. Are you sure you don't want to use
pdb2gmx (for proteins)?
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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