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

[Justin Lemkul]

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

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