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 <pachora...@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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