Hi! I am using the gromos9643a1 forcefield and the chloride is described as given below in the rtp file. I have described the CL as CL- in my pdb input file and still it is not accepting! I am using V 4.0.5
[ CL- ] [ atoms ] CL CL- -1.00000 0 [ bonds ] [ angles ] ; ai aj ak gromos type [ impropers ] ; ai aj ak al gromos type [ dihedrals ] ; ai aj ak al gromos type On Mon, Jun 28, 2010 at 4:15 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > jayant james wrote: > >> Hi! >> The protein I am attempting to simulate has a CL atom. When I run pdb2gmx >> I get the following error message. Any help in overcoming this problem would >> be appreciated. >> Thanks >> James ------------------------------------------------------ >> Program pdb2gmx, VERSION 4.0 >> Source code file: pdb2gmx.c, line: 429 >> >> Fatal error: >> Atom CL- in residue CL- 574 not found in rtp entry with 1 atoms >> while sorting atoms >> ------------------------------------------------------- >> > > You haven't told us which force field you're trying to use, but I'm > guessing that the chloride .rtp entry is probably named "CL" instead of > "CL-" (which is used by the ffG* force fields). You can check the .rtp file > to be sure. > > Also, I would strongly suggest upgrading to version 4.0.7 - there have been > numerous bug fixes and performance upgrades since version 4.0. > > -Justin > > >> >> -- >> Jayasundar Jayant James >> >> www.chick.com/reading/tracts/0096/0096_01.asp < >> http://www.chick.com/reading/tracts/0096/0096_01.asp>) >> >> > -- > ======================================== > > 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 > -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp)
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