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

SOMNATH JAN jansomnath at gmail.com
Tue Jul 4 07:01:35 CEST 2017

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.

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