[gmx-users] 5' Phosphate (5PHO) patch for RNA in CHARMM36 forcefield - Gromacs

Justin Lemkul jalemkul at vt.edu
Wed Jul 5 14:52:23 CEST 2017

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 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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