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 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

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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