Hello Mr. Bill
Thank you. Thank you very much
Sanjib.
On Thu, Sep 6, 2012 at 5:48 PM, Bill Miller III <brmilleriii.gmail.com>wrote:
> Yes, you can use the -cp flag to specify the prmtop file for stability
> calculations (calculations without a receptor or ligand).
>
> -Bill
>
>
>
> On Sep 6, 2012, at 6:59 AM, Sanjib Paul <sanjib88paul.gmail.com> wrote:
>
> > 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
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> >>
> >
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Received on Thu Sep 06 2012 - 06:00:03 PDT
