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.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.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.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Wed Jul 08 2009 - 08:35:35 PDT
