Just thinking out loud, but maybe "Argon" is too long of a name for the residues. The longest I think I've seen is 4 characters (something like LYSH or ARGN, for example). Maybe the length of the name is throwing off the formatting. Why don't you try again with a residue name of something like AR (in both the .top and .gro, of course) and see if that fixes things.
-Justin Quoting Andreas Kring <[EMAIL PROTECTED]>: > Hello all. > > I'm trying to simulate an argon liquid. The OPLS-AA force field is used > with the files from /usr/local/gromacs/share/gromacs/top. But I get an > error when I run > > $ grompp -f NVT.mdp -c Ar.gro -p Ar.top > ------------------------------------------------------- > Program grompp, VERSION 3.3.3 > Source code file: confio.c, line: 709 > > Fatal error: > Invalid line in Ar.gro for atom 1: > 1Argon Ar 1 0.0 0.0 0.0 > ------------------------------------------------------- > > An ideas on what can be wrong? My argon .top file and .gro file can be > seen below. > > Kind regards > Andreas > > ---------------------- > Ar.top > ---------------------- > ; Topology file for Ar > > ; Parameter level > > #include "ffoplsaa.itp" > ; #define _FF_OPLS > ; #define _FF_OPLSAA > ; [defaults] > ; #include "ffoplsaanb.itp" > ; [atomtypes] > ; #include "ffoplsaabon.itp" > ; [bondtypes] > ; [constrainttypes] > ; [angletypes] > ; [dihedraltypes] > > ; Molecule level > > [ moleculetype ] > ; molname nrexcl > Argon 1 > > [ atoms ] > ; id at_type res_nr res_name at_name cg_nr charge > 1 opls_097 1 Argon Ar 1 0.0 > > ; System level > > [ system ] > Argon liquid > > [ molecules ] > Argon 2048 > > --------------------------------- > Ar.gro > --------------------------------- > fcc lattice of argon atoms > 2048 > 1Argon Ar 1 0.0 0.0 0.0 > 2Argon Ar 2 0.283835 0.283835 0.0 > ... > 2047Argon Ar 2047 4.257525 3.97369 4.257525 > 2048Argon Ar 2048 3.97369 4.257525 4.257525 > 4.54136 4.54136 4.54136 > > _______________________________________________ > gmx-users mailing list gmx-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 > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list gmx-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
