Hello Mr. Jason,
In MMPBSA.py command line there is no -p flag
to specify prmtop file. The system I am using is a protein only, not a
complex. It is a metalloprotein. Here I have used -cp flag to
introduce prmtop file. Can I use it safely?
Sanjib
On 9/5/12, Jason Swails <jason.swails.gmail.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 06 2012 - 04:30:04 PDT
