[gmx-users] error in phosphoserine simulation during MD

[Justin Lemkul]

On 6/17/17 4:05 PM, marzieh dehghan wrote:
> Hi
> 
> Dear all
> 
> I want to simulate a protein containing phosphoserine using MD, so I place
> the force field into the working directory and modified all parameters of
> force field for example SEP (phosphoserine) was added as Protein in the
> residuestypes.dat , but I confronted the following error?
> 
> Atom N is used in an interaction of type improper in the topology database,
> but an atom of that name was not found in residue number 3.
> 

Can you please provide your exact pdb2gmx command and the full screen output? 
There's a lot of potentially diagnostic information there.  You also may simply 
be missing atoms - not all experimental structures are complete and are clearly 
indicated by MISSING lines in the PDB file.

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

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