[gmx-users] Energy Calculation

[Ing. Vojtech Spiwok]

> On Fri, 2004-06-25 at 08:10, Gaurav Porwal wrote:
> > Hi,
> >
> > When I'm trying to calculate the energy of a predicted structure of an
85
> > residue protein, i'm getting the following error by pdb2gmx and all the
> > subsequent commands fail (run via a shell script):
> >
> > Fatal error: Incomplete ring in HIS68
> And have you checked whether this is correct?
>
> pdb2gmx can only treat "normal" proteins, so if you're missing atoms
> it's a problem.

If you start from the crystal structure downlloaded directly from
pdb there could be two side-chains of one amino-acid (both
sidechains are visible in electron density map but I do not
remember how crystalographers call this) or side-chain could
be missing. If this is first case than chose one and delete the second,
if this is the second case try SCWRL or swiss-pdb-viewer.
http://www.expasy.org/spdbv/
http://dunbrack.fccc.edu/SCWRL3.php

cheers
Vojtech Spiwok

> >
> > Is there a way in which I can calculate/minimize this energy. I've tried
> > using -missing flag in pdb2gmx but that doesn't work. Plz. help.
> >
> > Thanks in advance.
> >
> > Regards,
> > Gaurav
> >