[gmx-users] 5' phosphate of RNA

Justin Lemkul jalemkul at vt.edu
Tue Jul 11 19:05:22 CEST 2017

On 7/11/17 7:06 AM, mohammad fathabadi wrote:
> Thank you Justin
> I saw SOMNATH question and your answer about 5' PHO on 5 Jul.
> According that answer,  I  put PRES 5 PHO from  top_all36_na.rtf   file in merged.n.tdb  file after [5TER] section but I receive many errors like: Atom NA not found in  1GUN buiding block wile rtp and itp Atom N not found in  1GUN buiding block wile rtp and itp Atom C not found in  1GUN buiding block wile rtp and itp In my opinion I put 5 PHO patch in wrong position. where should I put this patch in merged.n.tdb file correctly  and it is neccesory that edit [5TER] section in this file.I have used CHARMM36(2017) for gromacs.Thank you for any advice

I don't know what residue "GUN" is, but it looks like pdb2gmx is trying to treat 
it as a protein, which means you didn't add it correctly as an entry in 
residuetypes.dat.  Beyond that, I can't comment on how you might have 
implemented the patch, so you'll have to provide more details.


> Regards
> On Tuesday, June 20, 2017, 5:27:45 AM GMT+4:30, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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


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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