On Wed, Sep 5, 2012 at 8:59 AM, Sanjib Paul <sanjib88paul.gmail.com> wrote:
> Dear Amber Users,
> I want to calculate normal modes of my
> system by NAB using AmberTools12. My input file is like following.
>
> molecule m;
> float x[4103], fret;
>
Your coordinate array must be set to hold 3*natom coordinates. If you have
4103 atoms, you will need an array with 12309 floating point values.
Otherwise you will get a segfault.
readparm(m,"protein.prmtop");
>
The molecule "m" needs to be initialized with a PDB file first, I believe.
> mm_options("cut=99., ntpr=50");
> mme_init(m, NULL, "::z", x, NULL);
> setxyz_from_mol(m, NULL, x );
>
> // conjugate gradient minimization
> conjgrad(x, 3*m.natoms, fret, mme, 0.1, 0.001, 2000);
>
You should probably use the xmin minimizer to prepare for normal mode
analysis -- it does a much better job of getting close to a minimum.
My suggestion is to either use MMPBSA.py to do your nmode calculations for
you, or look at mmpbsa_entropy.nab in $AMBERHOME/AmberTools/src/mmpbsa_py
and either use that program directly or adapt it for your needs.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Sep 05 2012 - 06:30:05 PDT
