Thanks Justin for the quick hint! So, only the last two columns are needed. Sorry for the stupid question, where can I obtain reliable values for the atomic van der waals radii? Is it I have to calculate from the original force field parameters, in my case, the opls?
Corina On Fri, Oct 25, 2013 at 12:04 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 10/24/13 12:02 PM, Corina Mo wrote: > >> Dear Gromacs users, >> >> I am interested to do implicit solvent MD but I find that some atoms >> (atomtype opls_961-965) in my system does not have parameters in the file >> gbsa.itp. >> >> Does anyone know the meaning of these columns in the file and the proper >> way >> to derive these values? >> ; atype sar st pi gbr hct >> >> > Manual section 5.3.5 has a complete explanation and relevant literature > references. > > -Justin > > -- > ==============================**==================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu> | > (410) > 706-7441 > > ==============================**==================== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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
