Thank you Justin... 1] I have created an Ammonia molecule from Avogadro software...and saved it in .pdb file format... 2] Than gave the command gmx pdb2gmx -f ammonia.pdb -o ammonia.gro 3] There im not getting the CGenFF force field/r CHARMM36 port..., my gromacs version is 5.0.7.., How to get/install this force field..? 4] I just ant to simulate ammonia .. and i dnt want water, so i have not give -spce command @ the end as - gmx pdb2gmx -f ammonia.pdb -o ammonia.gro instead of gmx pdb2gmx -f ammonia.pdb -o ammonia.gro -water spce. Hope this is right command...
Sent with Mailtrack <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.di...@nitk.edu.in&idSignature=22> On Tue, Jan 17, 2017 at 12:19 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/16/17 2:44 AM, Dilip H N wrote: > >> My questions are.. >> 1] how to create a topology file for ammonia.?? >> 2] how to create a force field for ammonia, what is the residue name for >> ammonia in .pdb file.?? >> 3] Why ammonia.itp is not there in gromacs..?? >> 4] Which force field to choose for ammonia..?? >> >> > The CHARMM General Force Field (CGenFF) supports ammonia. Its residue > name is AMM1 and it is in our CHARMM36 port for GROMACS. Use pdb2gmx on a > suitably named coordinate file and you've got your topology. > > http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs > > -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. > -- With Best Regards, DILIP.H.N Ph.D Student, Research Scholar, Department of Chemistry, National Institute of Technology-Karnataka, Surathkal, Mangaluru - 575025. -- 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.