What does your topology (.top) file look like? And what's the exact command you are using for grompp?
-- James “Wes” Barnett Ph.D. Candidate Chemical and Biomolecular Engineering Tulane University Boggs Center for Energy and Biotechnology, Room 341-B New Orleans, Louisiana 70118 jbarn...@tulane.edu LinkedIn ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Rasha Alqus <rasha.al...@manchester.ac.uk> Sent: Wednesday, June 3, 2015 8:39 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Atomtype OW not found Dear Gromacs users, I am trying to run an md of carbohydrate systems in water, the pdb of carbohydrate produced in glycame builder, files were loaded in amber to produce topolgy file and coordinate using glycame force file. I have run glycam2gmx.pl script to convert files into gromacs ones. I would like to solavte the sytem using tip5p, but when i run the grompp i get an error program grompp_d, VERSION 4.5.4 Source code file: toppush.c, line: 1166 Fatal error: Atomtype OW not found For more information and tips for troubleshooting, please check the GROMACS I also tried to do that with other water model and it give me the same issue, can you please help me to solve that issue. Thank for the help Regards rasha -- 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. -- 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.
