Re: [gmx-users] error in topology file
Dear all gmx users and developers, The structure of mine is: C-C-C-C-C-C-C-C-C=C-C-C-C-C-C-C-C-C-O | C-C-C-C-C-C=C-C-C=C-C-C-C-C-C-C-C-C=O * The warning appeared during grompp was at the carbon with symbol star. I try the possible force field but still cant get the correct one. I am using OPLS-AA force field for my simulation. Any suggestions to replace the correct value? Any suggestions and comments are appreciated. Thanks. --- David van der Spoel <[EMAIL PROTECTED]> wrote: > huan wrote: > > Dear all gmx users and developers, > > > > After i run the grompp, there were two warnings > > appeared. The warning statements are as follow: > > > > warning 1 [File "p1.top" line 208] > > No default Ryckaert-Bell. type, using > zeros. > > > > warning 2 [File "p1.top" line 209] > > No default Ryckaert-Bell. type, using > zeros. > > > > I checked the lines as stated in the warning, but > i > > didn't realize what is the problems. > > > > Any suggestions and solutions are appreciated. > you are missing force field parameters at the > indicated lines. > > > > THANKS. > > > > > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > http://www.gromacs.org/search before posting! > > 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 > > > -- > David van der Spoel, Ph.D., Professor of Biology > Molec. Biophys. group, Dept. of Cell & Molec. Biol., > Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. > Fax: +4618511755. > [EMAIL PROTECTED] [EMAIL PROTECTED] > http://folding.bmc.uu.se > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/search before posting! > 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 listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
RE: [gmx-users] Error in topology file
This will be helpful for you: http://wiki.gromacs.org/index.php/Exotic_Species and other information from gromacs wiki. Andreas From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of s lal badshah Sent: 16 April 2008 11:12 To: gromacs Subject: [gmx-users] Error in topology file Dear Experts, Hi ! I am doing simulation of cholera toxin, one with GTP( guanosine triphosphate) and other without it.The without GTP MD simulation I have done, now I started the other and when I used the pdb2gmx command on pdb file it says: Program pdb2gmx, VERSION 3.3.1 Source code file: resall.c, line: 438 Fatal error: Residue 'GTP' not found in residue topology database Earlier this already happen so I left that and was started the pdb having GTP removed but this time it is necessary for me.Should I use prodrg server or some thing else. Hoping for guidance. Lal badshah. Send instant messages to your online friends http://uk.messenger.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
Re: [gmx-users] error in topology file generation
Archana Chavan wrote: /hello everybody,/ /i am new user to GROMACS,/ /i want to perform simulations on docked protein ligand complex,/ /During the conversion of the PDB file i came to such a problem: //just before the end of conversion the program pdb2gmx.exe told that my //PDB file compound is not included into Gromacs residue topology database. //Directly as it says: //" Fatal error: Residue ''M_3' not found in residue topology database "/ (which is docked ligand in the protein) /Woud you be so glad to tell me how can I resolve this problem? / chapter 5 in the manual. looking forward to your help tahnks in advance. -- Archana Chavan MS (Pharm)Pharmacoinformatics National Institute of Pharmaceutical Education and Research (NIPER) Mohali-160 062 Punjab, India. phone:+91-(0)-947223 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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 -- 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 listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
