[gmx-users] pdb2gmx conversion

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Oct 28 11:30:39 CET 2013

Hi Musyoka,

I would guess that that is related to the input coordinates. A bit of EM
should fix it.



On Mon, Oct 28, 2013 at 11:20 AM, MUSYOKA THOMMAS <
mutemibiochemistry at gmail.com> wrote:

> Dear Users,
> Whenever i convert a protein.pdb file using the following command (pdb2gmx
> -f protein.pdb -o protein.gro/pdb -water spc) and thereafter visualise the
> output with either vmd or pymol, i get the first amino acid residue
> breaking from the main chain.
> Would anyone help me understand why this is happening?
> Thanks.
> --
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Tsjerk A. Wassenaar, Ph.D.

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