AMBER Archive (2009)

Subject: Re: [AMBER] unsolved verbosity when running minimization

From: albert albert (albertassonke_at_googlemail.com)
Date: Wed Jul 08 2009 - 06:10:43 CDT

Dear Carlos,

yes, I have a very high energy. My problem it is to find a way to modify my
structure without get out of the real assembly of this complex.

My structure is PEA LIGHT-HARVESTING COMPLEX II AT 2.5 ANGSTROM
RESOLUTION<http://www.rcsb.org/pdb/explore.do?structureId=2BHW>
I take it from protein data bank, my goal is to perform a molecular dynamic
simulation and some quantum calculation.

Maybe I have missed something in amber10 Book: BPTI.

I am running a minimization with your suggestion....

thanks for all

Regards

Albert
**

On Mon, Jul 6, 2009 at 9:28 PM, Carlos Simmerling <
carlos.simmerling_at_gmail.com> wrote:

> it looks like you have a high energy in your structure, a bond that is very
> distorted. what do you mean by the verbosity? do you want less information?
> ntpr determines how often it writes the energy info.
>
> On Mon, Jul 6, 2009 at 3:09 PM, albert albert
> <albertassonke_at_googlemail.com>wrote:
>
> > Dear Amber10 users,
> >
> > Greetings.
> >
> > I am receiving the following error, when running a short test of
> > minimization.
> >
> >
> > NSTEP ENERGY RMS GMAX NAME NUMBER
> > 1 6.8820E+07 NaN 4.8579E+08 O 6909
> >
> > BOND = 331518.9485 ANGLE = 122306.0419 DIHED =
> > 25856.5243
> > VDWAALS = 29603626.4080 EEL = -157089.9138 EGB =
> > -11490.7944
> > 1-4 VDW = 38871594.5924 1-4 EEL = 33205.3388 RESTRAINT =
> > 0.0000
> >
> >
> > I didn't understand the origin of this verbosity in my MPI.
> >
> >
> > Regards
> >
> > Alabert
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> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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