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

Pacho Ramos pachoramos at gmail.com
Wed Dec 4 11:33:21 CET 2013

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?


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