[gmx-users] pdb2gmx warning

[Justin Lemkul]

On 7/26/15 6:55 AM, faride badalkhani wrote:
> Dear all,
> I am performing a simulation on a plymeric structure, and I can exwcute
> pdb2gmx command successfully but there are some warnings as follows:
>
> Warning: Starting residue AMC1 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue AMI2 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue AMI3 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue AMI4 in chain not identified as Protein/RNA/DNA.
> Warning: Starting residue AMI5 in chain not identified as Protein/RNA/DNA.
> More than 5 unidentified residues at start of chain - disabling further
> warnings.
> Problem with chain definition, or missing terminal residues.
> This chain does not appear to contain a recognized chain molecule.
> If this is incorrect, you can edit residuetypes.dat to modify the behavior.
>
>
> How can I solve this problem?
>

It's not actually a problem; warnings and notes are informative ("hey user, 
check and make sure this is right!").  Errors are problems.

You've got a polymer that is not a known biomolecule.  pdb2gmx simply does this 
check to determine how to treat the molecule and make sure you're not mixing 
things strangely.

-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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