[gmx-users] residuetypes.dat file problem

[Justin Lemkul]

On 2/18/17 12:41 PM, Mishelle Oña wrote:
> Hello everyone,
>
> I am modifying a force field to simulate a Polymer. I have add the monomers of my polymer in residuetypes.dat file as follows:
>
> ETHB      Polymer
>
> ETHP      Polymer
>
> ETHE      Polymer
>
> When I run the pdb2gro command a message like this appears:
>
> Processing chain 1 (153 atoms, 30 residues)
> Warning: Starting residue PLAB1 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue PLAP2 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue PLAP3 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue PLAP4 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue PLAP5 in chain not identified as Protein/RNA/DNA.
> More than 5 unidentified residues at start of chain - disabling further warnings
>
> Please could you help me with this problem?
>

There isn't a problem.  pdb2gmx is being a little too noisy in this instance, 
but it is true that "Polymer" is neither Protein, DNA, nor RNA.  You don't 
necessarily have to do anything in residuetypes.dat for a polymer system.

-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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