[gmx-users] A simple question
s_poorasad at yahoo.com
Tue Apr 14 03:00:02 CEST 2015
Dear Dr.Smith ,
Thanks for your replay .
This is a part of my PDB file :
ATOM 1 CD1 TRP 1 19.910 19.430 16.500 1.00 0.00ATOM 2 CD1 TRP 1 20.210 20.850 16.560 1.00 0.00ATOM 3 CD1 TRP 1 19.010 21.540 16.970 1.00 0.00ATOM 4 CD1 TRP 1 17.960 20.560 17.150 1.00 0.00ATOM 5 CD1 TRP 1 18.520 19.250 16.860 1.00 0.00ATOM 6 CD1 TRP 1 19.090 22.640 17.820 1.00 0.00...I want to define C-delta atom of the aromatic tryptophan amino acid for C60 carbons and i want to use oplsaa force field.
Best regards ,Saeed.
From: "Smith, Micholas D." <smithmd at ornl.gov>
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>; saeed poorasad <s_poorasad at yahoo.com>
Sent: Monday, 13 April 2015, 21:24
Subject: Re: [gmx-users] A simple question
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
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.
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