You CAN'T, of course
basically, MMPBSA does not move any atoms, nor does it compute/use any
forces. It simply postprocess what you have already done with the
dynamics itself.
So, the large VDW energies out of scale you see (I am not even sure what
that means, can you clarify?) cannot come from ntc=2 or anything like that.
I bet that what you have are incompatible prmtop/crds.
Adrian
On 11/15/10 3:01 PM, Jose Borreguero wrote:
> Dear Amber users,
>
> I'm having trouble using MMPBSA on a simulation that was carried out with
> rigid bonds involving hydrogens. The Van der Waals computed energy by MMPSBA
> is out of scale. I though of including the 'ntc=2' option in the following
> mmpbsa.in file:
>
> *&general
> endframe=2525, verbose=1,
> entropy=0,
> ntc=2,
> /
> &gb
> igb=2, saltcon=0.100
> /
> &pb
> istrng=0.100, fillratio=2.0, scale=1.0
> /*
>
> Unfortunately, the option 'ntc=3' is not understood by the parser. Does
> anyone has an idea of how can I call for rigid bonds in MMPBSA ?
>
> Best regards,
> Jose M. Borreguero
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project, Department of Chemistry
University of Florida
Senior Editor. Journal of Physical Chemistry.
on Sabbatical in Barcelona until August 2011.
Email roitberg.ufl.edu
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Received on Mon Nov 15 2010 - 07:00:03 PST
