Hi David, I don't see the source of error in the pdb format of the file. I can visualize it with any program and the oxygen is there. The problem appears when I want to create the .gro file form the pdb2gms program. I am trying to bind a oxygen atom to the sulfur atom of the MET residue. The pdb2gmx complains, although I have tried several different options. The oxygen atom is not a part of the MET residue database. Is these any way to overcome that or I just need to redifine a new residue type, like METO, in the residue database?
Thank for your answer, Sincerely Luciano Dr. Luciano Triguero College of Art and Science Department of Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box 249118 Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office: 305-284-3938 -----Original Message----- From: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Fri 2/23/2007 4:42 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Advices needed! Triguero, Luciano O wrote: > Hi Everyone, > > I need your help in the following matter. How do I generate a .gro file from > a pdb file where I added an oxygen atom to > one of the residue? > > I get the following error message when I run pdb2gmx: > > ======================================= > Program pdb2gmx, VERSION 3.3.1 > Source code file: resall.c, line: 438 > > Fatal error: > Residue '' not found in residue topology database > ======================================== > you probably have made an error in the format of the file. -- 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 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list [email protected] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list [email protected] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
