Dear gromacs users, Dr. Justin, I managed to run md simulation with the aid of your helps here . As the next step I'm trying to create a crystal from polymer molecule so i can put several molecules to the same box and do a simulation. What approach should I take here ?
Regards Sameera Edirisinghe On Sep 22, 2016 00:41, "Justin Lemkul" <jalem...@vt.edu> wrote: > > > On 9/21/16 7:42 AM, Sameer Edirisinghe wrote: > >> Dear Dr. Justin, >> >> Thanks for the explanation. Now i got the point you mentioned here. Then i >> checked the bonds i have mentioned in .rtp file and then i found the >> relevant bonded type. then i checked the ffbonded.itp file and i found >> that >> bond type is already in there. >> As an example, >> >> CAY HA1 ; this is one of bond i have in .rtp file. and for that bond, >> relevant bond type (mentioned as below) was already in ffbonded.itp file >> CT HC 1 0.10900 284512.0 >> >> But still following error is occurring while running grompp. >> >> 1) ERROR 1 [file topol.top, line 108]: >> No default Bond types >> >> 2) ERROR 2 [file topol.top, line 168]: >> No default Angle types >> >> 3) ERROR 3 [file topol.top, line 426]: >> No default Ryckaert-Bell. types >> >> How do i refer particular bond types in ffbonded.itp file to my current >> .gro file or any other relevant file ? >> >> > grompp won't complain about parameters being missing if they're actually > there. You're probably looking at the wrong line. > > -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 > > jalem...@outerbanks.umaryland.edu | (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 gmx-users-requ...@gromacs.org. > -- 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 gmx-users-requ...@gromacs.org.