Re: [AMBER] save Hessian nmode mmpbsa

From: Bruno Falcone <>
Date: Thu, 4 Aug 2016 12:45:51 -0300

Hi, any takers on my question?

I've been looking through the code and what I've found so far is the

MMPBSA uses nab for the nmode calculation. In
AmberTools/src/mmpbsa_py/ 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

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!


On 03/08/16 13:51, Bruno Falcone wrote:
> Hi, I need to save the Hessian that is obtained during the nmode
> calculation in, 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
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