Check out the AmberTools/src/sff directory -- there should be a nmode.c
file there, if I recall correctly.
That's where the nab implementation lives.
HTH,
Jason
On Thu, Aug 4, 2016 at 11:45 AM, Bruno Falcone <brunofalcone.qo.fcen.uba.ar>
wrote:
> 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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--
Jason M. Swails
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Received on Thu Aug 04 2016 - 11:00:02 PDT
