Dear Justin, Many thanks for your answer. I tried grep " SI " *.* in the whole working directory but nothing found. Where could it be if I have to search? Thanks a lot again. Regards, Jennifer
On Thu, Jan 15, 2015 at 6:44 PM, Justin Lemkul <[email protected]> wrote: > > > On 1/15/15 12:20 PM, Jennifer Vo wrote: > >> Dear Experts, >> I ran a grompp (gromos53a6 ff) >> grompp -f em.mdp -c complex2_solvated.gro -p topol.top -o complex.tpr >> >> and it generated the error >> Atomtype P,SI not found >> >> I checked the gromos53a6.ff/atomtypes.atp and see there are P, SI in the >> list >> SI 28.08 ; Silicon >> P 30.97380 ; Phosphor >> >> And there is no P, SI in my complex2_solvated.gro file! I really do >> appreciate for any help. >> > > It's an atom type, so it won't be in a coordinate file. Something in a > topology or force field file is specifying something called "P,SI" as an > atomtype. That's clearly not sensible. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > [email protected] | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
