I have addes the "CO" residue. Coordinate file REMARK Accelrys Discovery Studio PDB file REMARK Created: Fri May 28 17:26:23 Eastern Daylight Time 2010 HETATM 1 C1 CO 0 -1.044 -0.027 0.066 0.00 0.00 C HETATM 2 O2 CO 0 -0.009 0.642 -0.037 0.00 0.00 O HETATM 3 O3 CO 0 -2.286 0.595 -0.030 0.00 0.00 O END
in ffopla.rtp file. [ CO ] ; mandatory [ ATOMS ] ; mandatory C1 opls_974 1.00 1 O2 opls_975 -0.50 2 O3 opls_976 -0.50 2 [ bonds ] C1 O2 C1 O3 I have also addes new atoms typs in ffopls.atp file. NIlesh On Tue, June 1, 2010 3:35 pm, Justin A. Lemkul wrote: > > > Nilesh Dhumal wrote: > >> Hello, >> >> >> I am getting the following error during pdb2gmx. >> >> >> Fatal error: Atom O in residue CO 1 not found in rtp entry with 3 atoms >> while sorting atoms >> >> I checked the pdb file and ffopls.rtp file also. >> >> > > And what did you find? To my knowledge there is no such residue "CO" in > the ffoplsaa.rtp file. Is this something you've added? Regardless, > there's a mismatch somewhere, so if you can't identify it, post the text > of your coordinate file and the relevant .rtp entry to see if someone else > can spot it. > > -Justin > > >> Nilesh >> >> >> >> >> > > -- > ======================================== > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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
