You can always see if you have any by looking at cgnr column of the protein .itp file. If each atom is in its own chargegroup (the cgnr increments by atom) then it's fine.
Is this charmm36 (when did you install this from the website?)or 27 (what gromacs version)? There were two chargegroup problems fixed in two successive versions. First, I think 4.5.4 Charmm27 removed all chargegroups for by default in the .rtp files. Then, the charmm36 upload was fixed to do that too. However, I am not sure what versions has fixed terminii. In gromacs 4.5.3 and the charmm36 from that time period would generate capping groups with a single large chargegroup. Anyway, Grompp will give you an idea if you have a really large chargegroup when it gives you the notice about them; if your largest chargegroup is comparable to the van der waals diamater of two atoms I don't think there is anything to worry about. If you do have a lot of large chargegroups, apparently you might run into cutoff artifacts but I'm not sure exactly. On 2012-12-20 01:37:25PM +0300, James Starlight wrote: > Peter, > > what errors might occurs if I've missed -nochargegrp option while > parametrising my protein by means of pdb2gmx? > > > James > > > 2012/12/20 Peter C. Lai <p...@uab.edu>: > > (As a side note, Gromacs shouldn't use charge groups when using > > all-atom charmm forcefields.) > -- > 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists