[gmx-users] Topology file for Fullerene with OPLS_AA force field

Smith, Micholas D. smithmd at ornl.gov
Wed Apr 15 14:21:47 CEST 2015

As Justin mentioned in an earlier response you aren't going to be able to use pdb2gmx for this, instead you are going to need to use x2top if you are going to build your own topology. Alternatively, you may have better luck building one by hand (see the gromacs manual, and be prepared to spend a day building and testing until you have the "right" one).

 I have checked the snipit of the pdb you sent me and that seems fine. I currently don't have access to my old topologies (as a collaborator and myself did some work with fullerene-like systems), but I can assure you that it is possible to build one.

I would suggest you contact Dr. Luis Cruz Cruz of Drexel University ( ccruz at drexel.edu ) and see if he has any students still working on fullerene systems, as they may have topologies you can use.

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: Wednesday, April 15, 2015 2:51 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] Topology file for Fullerene with OPLS_AA force field

Hi Gromacs users ,
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.

this is a part of my PDB file : HETATM    1  CD1 TRP     0       3.341   0.669   0.088  1.00  0.00           CHETATM    2  CD1 TRP     0       3.266  -0.548  -0.502  1.00  0.00           CHETATM    3  CD1 TRP     0       2.990  -1.662   0.229  1.00  0.00           CHETATM    4  CD1 TRP     0       2.750  -0.402  -1.741  1.00  0.00           C
I have no experience with GROMACS , so I will be grateful if you can help me .
Best ,Saeed.
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