[gmx-users] files missing

[Rahul Karyappa]

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

India

-- 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
>
> *****************************************************************
> This email is virus free by TrendMicro Inter Scan Security Suite.
> *****************************************************************
>
Which gromacs version?
I'm attaching the ffgmx version. Are you sure you don't want to use
pdb2gmx (for proteins)?
--
David.
________________________________________________________________________
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.

*****************************************************************
This email is virus free by TrendMicro Inter Scan Security Suite.
*****************************************************************
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20050811/a74a709d/attachment.html>