Thanks for the response Jason. I have tried the fixes suggested in
http://structbio.vanderbilt.edu/archives/amber-archive/2009/5852.php Then
I recompiled AMBER. Yet I am getting the same error
" bad atom type: Co
CalcError: /home/suchetana/Downloads/amber12/bin/sander failed with prmtop
complex.top!"
Any suggestions?
Thanks
On Tue, Aug 4, 2015 at 6:22 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, 2015-08-04 at 11:53 +0530, MOHD HOMAIDUR RAHMAN wrote:
> > Dear Amber Users
> >
> > I have a metalloprotein (Co2+) complex bound to the substrate. I have
> > generated trajectory 60ns MD run using AMBER. Now I am planning to do
> > binding energy calculation for ligand-protein. I use AMBER12. Using
> > antechamber I got the necessary complex, ligand and receptor topology
> > files. However when I try to run MMPBSA.py, the error that i am getting
> is
> > bad atom type.
>
> Try putting the error message into Google. This problem has been
> addressed many times in the past, and there are several posts that
> explain how to fix it that should come up following a simple search.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Tue Aug 04 2015 - 23:00:02 PDT
