[gmx-users] A simple question

Smith, Micholas D. smithmd at ornl.gov
Mon Apr 13 14:26:06 CEST 2015

Hi Saeed,

Attachments don't work with the mailing list. Could you copy a few lines of the pdb for us to look at and maybe upload the pdb you generated to dropbox or a similar site?

Also pdb2gmx may not be the best route here. You may need to explicitly write your own topology file (tedious as it may be), but lets take a closer look at what your pdb first.

Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of saeed poorasad <s_poorasad at yahoo.com>
Sent: Monday, April 13, 2015 2:29 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] A simple question

Hi .
Dear Gromacs users .
Today is the first day that i am working with GROMACS .I want to have a system with one C60 and about 1000 water molecules .I tried to use pdb2gmx on C60.pdb but I got fatal error , I think the problem is because of my PDB file .I want to define C-delta atom of the aromatic tryptophan amino acid for C60 carbons and i want to use oplsaa force field.
Can you please let me know what the problem is ?
I have attached my PDB file with this Email.
Best ,Saeed.

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