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." <smit...@ornl.gov> To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>; saeed poorasad <s_poora...@yahoo.com> Sent: Monday, 13 April 2015, 21:24 Subject: Re: [gmx-users] A simple question 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-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of saeed poorasad <s_poora...@yahoo.com> Sent: Monday, April 13, 2015 2:29 AM To: gmx-us...@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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.