since you are using sander and sander is free, I highly recommend to
install AmberTools15.
http://ambermd.org/#AmberTools
Hai
On Wed, Aug 5, 2015 at 1:51 AM, MOHD HOMAIDUR RAHMAN <rahmanhpu.gmail.com>
wrote:
> 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Tue Aug 04 2015 - 23:00:02 PDT
