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

Pacho Ramos pachoramos at gmail.com
Wed Dec 4 11:35:04 CET 2013

Looks like I am unable to attach the offending pdb file because mailing
list imposes a size limit of 50 Kb for the whole message (including
attachments) and the file is around 1 MB, what way do you prefer for
providing the file?

Thanks for the info

2013/12/4 Pacho Ramos <pachoramos at gmail.com>

> 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?
> Thanks

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