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

[Justin Lemkul]

On 12/4/13 11:22 AM, Pacho Ramos wrote:
> 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
>

Check what those atoms are and whether or not they should be bonded.  If they're 
just two molecules or residues that are spatially proximal, there's nothing 
wrong.  If there is some distorted geometry leading to a strange bond, then 
energy minimization should take care of it.

For what it's worth, VMD throws this message all the time and it rarely means 
anything.  Your topology within Gromacs is definitive.  External software is not.

-Justin

>
>
> 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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-- 
==================================================

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

==================================================