He didn't have a CC: to smit...@cancer.org.uk so he probably felt he had to resubmit the question, LOL.
Jim -----Original Message----- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul Sent: Friday, July 24, 2009 7:22 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] error in ffG43a1p force field Thamu wrote: > Hi, > > i am trying to run md for protein-peptide complex. the peptide has > phosphorylated tyrosine. > > i got the following error when i run pdb2gmx > > Fatal error: > Error in hdb file ffG43a1p.hdb: > Wrong number of control atoms (2 iso 3) on line: So, did you follow Mark's advice and read section 5.6.2? Repeating a question without reference to previous help is usually a fast way to get ignored. Demonstrate that you are willing to help yourself before you expect to get more free help :) This is indeed a formatting issue. The ffG43a1p force field was designed for use with Gromacs-3.1.x, when formatting of these files was slightly different. They are quite easy to fix, if you read the manual. -Justin > 1 1 N -C CA > > I also tried with phosphoserine, i got the same error as for > phosphotyrosine. > I am using gromacs-4.0.2. > > > I would greatly appreciate if some one help me to solve this error. > > Thanking you, > > Yours sincerely, > Thamu > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php