[gmx-users] Fwd: Warning while loading .gro generated from .pdb with pdb2gmx

[Pacho Ramos]

Thanks for your reply. Anyway, looks like every pdb I convert using above
command leads to this warning, for example, when I try with 1TIT:
http://www.pdb.org/pdb/explore/explore.do?structureId=1TIT

I also get the same kind of warning while loading generated .gro file,
telling me that something is "strange" with the last residue.

Maybe gromacs is using a different nomenclature inside the generated .gro
file that VMD is failing to understand, but the problem looks to appear in
all cases I have tested



2013/12/4 Justin Lemkul <jalemkul at vt.edu>

>
>
> On 12/4/13 5:33 AM, Pacho Ramos wrote:
>
>> When I convert attached .pdb file to .gro using:
>> pdb2gmx  -quiet -ff amber99 -water none -f ${MOL}.pdb -o ${MOL}Initial.gro
>> -i ${MOL}.itp -p ${MOL}.top -ignh
>>
>> the generated .gro file causes vmd (1.9.1) to show this warning while
>> loading it:
>> Warning) Unusual bond between residues:  905 (protein) and 906 (none)
>>
>> Should I wonder about it? Or is pdb2gmx (from gromacs 4.6.2) generating a
>> wrong .gro file for some reason?
>>
>>
> What VMD thinks about bonds is irrelevant.  See http://www.gromacs.org/
> Downloads/Related_Software/Visualization_Software#
> Topology_bonds_vs_Rendered_bonds.
>
> You have two atoms that are close enough together that VMD guesses there
> should be a bond, but the "bond" occurs between chemically distinct
> entities, so it warns you.  It's not an important message in most cases.
>  For the purposes of the simulation, the only bonds that matter are the
> ones defined in the .top file.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
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