[gmx-users] 5' phosphate of RNA

[Justin Lemkul]

On 6/19/17 8:55 AM, Mohammad fat habadi wrote:
> DEAR Users
> I have a RNA that has phosphate(P,OP,OP2,OP3) on 5’.
> IN RNA and DNA, 3’ has phosphate and 5‘ doesn’t it and for this all Force fields don’t know phosphate atoms on 5’ of RNA.
> pdb2gmx  make an error.
> IF I delete 5’ phosphate atoms, I don’t have any problems.
> How can I solve this problem without deleting 5’ phosphate.

To keep the phosphate, you need to add a suitable rna.n.tdb entry in whatever 
force field you're using.  Most force fields may not support this.  CHARMM does, 
but it's not implemented in the GROMACS port.  You can get the parameters from 
the CHARMM force field files - look in top_all36_na.rtf (PRES 5PHO).

http://mackerell.umaryland.edu/charmm_ff.shtml#charmm

-Justin

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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