Re: [gmx-users] 5' Phosphate (5PHO) patch for RNA in CHARMM36 forcefield - Gromacs
On 7/4/17 12:31 AM, SOMNATH JAN wrote: Dear Users, I am trying to run a MD simulation in Gromacs using CHARMM36 forcefield for a RNA that has phosphate (P, OP1, OP2, OP3) on 5' . As the charmm36 forcefield doesn't recognize the phosphate atom (OP3) on 5' of RNA, pdb2gmx is giving an error. And so I want to add a 5'terminal PHOSPHATE patch (5PHO) in charmm36 forcefield. Parameters for 5PHO are available in CHARMM force field files in internet (top_all36_na.rtf - PRES 5PHO), but the charge units of atoms and the way of entry is completely different for CHARMM and Gromacs. So how will I make a new entry of 5PHO in Charmm36 by taking the parameters from CHARMM force field files? Another thing, there is no 'rna.n.tdb' file available for Charmm36 force field, so where will I make the new entry of 5PHO? You'll put it in merged.n.tdb - our port doesn't make a distinction between termini types (amino acids, DNA, RNA, etc). It's a limitation of how we generate the files. The information is almost identical to what one finds in the GROMACS files - atom names, types, and charges. You'll just have two blocks, [add] and [replace]. -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.
[gmx-users] 5' Phosphate (5PHO) patch for RNA in CHARMM36 forcefield - Gromacs
Dear Users, I am trying to run a MD simulation in Gromacs using CHARMM36 forcefield for a RNA that has phosphate (P, OP1, OP2, OP3) on 5' . As the charmm36 forcefield doesn't recognize the phosphate atom (OP3) on 5' of RNA, pdb2gmx is giving an error. And so I want to add a 5'terminal PHOSPHATE patch (5PHO) in charmm36 forcefield. Parameters for 5PHO are available in CHARMM force field files in internet (top_all36_na.rtf - PRES 5PHO), but the charge units of atoms and the way of entry is completely different for CHARMM and Gromacs. So how will I make a new entry of 5PHO in Charmm36 by taking the parameters from CHARMM force field files? Another thing, there is no 'rna.n.tdb' file available for Charmm36 force field, so where will I make the new entry of 5PHO? Thanks in advance. Regards, Somnath -- 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.
[gmx-users] 5' Phosphate (5PHO) patch for RNA in CHARMM36 forcefield - Gromacs
Dear Users, I am trying to run a MD simulation in Gromacs using CHARMM36 forcefield for a RNA that has phosphate (P, OP1, OP2, OP3) on 5' . As the charmm36 forcefield doesn't recognize the phosphate atom (OP3) on 5' of RNA, pdb2gmx is giving an error. And so I want to add a 5'terminal PHOSPHATE patch (5PHO) in charmm36 forcefield. Parameters for 5PHO are available in CHARMM force field files in internet (top_all36_na.rtf - PRES 5PHO), but the charge units of atoms and the way of entry is completely different for CHARMM and Gromacs. So how will I make a new entry of 5PHO in Charmm36 by taking the parameters from CHARMM force field files? Another thing, there is no 'rna.n.tdb' file available for Charmm36 force field, so where will I make the new entry of 5PHO? Thanks in advance. Regards, Somnath -- 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.
