Probably consult the tutorials to determine what T-coupling groups to use. Generally, Water_and_ions with a separate Protein as 2 T-coupling groups when dealing with a globular protein in water, but you will have to determine if that is appropriate for your particular system (i.e. if there are ligands, multi-molecule complexes, etc. involved it will probably be different).
On 2012-04-03 11:51:01AM -0700, Eduardo Oliveira wrote: > Hi all, > > After i ran grompp I've the following message: > > Fatal error: > 3 atoms are non part of any of the T-coupling groups > > It is probably in refference to the 3 CL atoms i've introduced into the > system to neutralize my protein charge. Here are the command lines for genion > and grompp > > genion_d -s arath_stpr.tpr -o arath_ions.gro -nname CL -nn 3 -nq -1 -p > arath.top > > grommp_d -f stpr.mdp -c arath_ions.gro -p arath.top -o arath_stpr.tpr > > Additional information: I'm running GROMACS 4.5.5 > > Regards. > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street [email protected] | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
