Hi, any takers on my question?
I've been looking through the code and what I've found so far is the
following:
MMPBSA uses nab for the nmode calculation. In
AmberTools/src/mmpbsa_py/mmpbsa_entropy.nab the call for the normal mode
calculation is done in line 72 through nmode(xyz, 3*natm, mme2, 0, 1,
0.0, 0.0, 0).
However, I was not able to find the definition of nmode anywhere else. I
looked in AmberTools/src/nab and there is a reference to it in nabcode.h
and another in symbol.c but these do not seem to contain the calculation
details.
I know that in previous versions of MMPBSA, the nmode.F90 program was
used for the normal mode calculation. I would be keen to use that one if
it is possible to modify it more easily to achieve the saving of the
Hessian onto a file. That code (src/nmode/nmode.F90) uses the forces.F90
subroutine to calculate the hessian. However, I'm not familiar with
Fortran, so if anyone could point me to the modifications I should do to
achieve saving the Hessian that would be great.
Thanks in advance for your help!
Bruno
On 03/08/16 13:51, Bruno Falcone wrote:
> Hi, I need to save the Hessian that is obtained during the nmode
> calculation in MMPBSA.py, to use it in a further calculation.
>
> Could you let me know how I can achieve that? What necessary
> modifications should I make to the code?
>
> Thanks!
>
> Bruno
>
>
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Received on Thu Aug 04 2016 - 09:00:03 PDT
