AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Jul 08 2009 - 06:34:20 CDT

the first place to look is your leap log and see if leap had to add any
heavy atoms. if atoms were missing from the density, leap may not build them
in an ideal place. also look for close contacts.
next you can look in a visualization program like VMD and check the region
around the atom noted in the "GMAX" in the min output file, in your case
#6909. that is the one with the highest force. fix that, and try again.
sometimes it can take several iterations to understand what is wrong with
the initial structure.

On Wed, Jul 8, 2009 at 7:10 AM, albert albert
<albertassonke_at_googlemail.com>wrote:

> 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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