[gmx-users] pdb2gmx warning
jalemkul at vt.edu
Mon Jul 27 02:20:16 CEST 2015
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
> 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
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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