I'll just make a small amendment to Jason's suggestion, which is that the
atom type OA describes an oxygen, so probably one of the oxygen types would
be more appropriate than carbon. OA is an aromatic heterocyclic oxygen, so
I would guess that the ether OS would probably be the best radius to use.
Cheers,
Brent
On Tue, Jan 20, 2015 at 8:19 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Tue, Jan 20, 2015 at 5:59 AM, Houcemeddine Othman <houcemoo.gmail.com>
> wrote:
>
> > Dear Amber users,
> > I have been trying to calculate the per residue free energy decomposition
> > of a protein-protein complex. The receptor protein is a metallaoenzyme in
> > which two zinc clusters were modeled using MCPB as described in the MTK++
> > documentation (HHHO and HHHD configurations). As far as I use only the PB
> > namelist the calculation run appropriately. However when adding the GB
> > section the following error message appears:
> >
> > Beginning GB calculations with /amber12/bin/sander
> > calculating complex contribution...
> > bad atom type: OA
> > CalcError: /amber12/bin/sander failed with prmtop
> > /home/free_energy_calculation/complex_vacum.prmtop!
> > Exiting. All files have been retained.
> >
> > Free energy estimation however were achieved successfully with either &PB
> > or &GB namelists.
> > Noting that i have amber12 compiled with AmerTools13 just three days ago
> (I
> > also tried it with AmbrtTools12 and it resulted to the same error).
> >
> > >From previous mail threads, it seems that only this one is relevant
> > http://archive.ambermd.org/201408/0262.html
> > However, I can not follow the same solution as it proposes to upgrade to
> > amber14 which is not available for me right now.
> >
>
> Why not? It's freely available at http://ambermd.org (for this, all you
> need is AmberTools 14, not Amber 14).
>
>
>
> > Can somebody help me to fix this problem in amber12 ?
> >
>
> Look for "bad atom type" in $AMBERHOME/src/sander/mdread.F90 (ca. line
> 2127). You need to add logic there to handle your new element. One option
> you have is to replace the error message and mexit call with a default
> radius assignment (I would, rather arbitrarily, choose the value for
> Carbon, personally). Then you need to recompile for those changes to take
> effect.
>
> A related post from a couple days ago:
> http://archive.ambermd.org/201501/0213.html
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
_______________________________________________
Brent P. Krueger.....................phone: 616 395 7629
Professor................................fax: 616 395 7118
Hope College..........................Schaap Hall 2120
Department of Chemistry
Holland, MI 49423
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Received on Tue Jan 20 2015 - 07:00:03 PST
