You can usually ignore errors like that if you are only minimizing for
equilibration purposes. Personally, I would run many fewer minimization
steps (1000-2000) and move on. There is little to be gained from performing
that many steps (and much to be lost in terms of errors).
Regards,
Brian
On Tue, May 20, 2014 at 9:46 AM, Valentina Romano <
valentina.romano.unibas.ch> wrote:
> Hi
>
> I changed the magnitude of the improper angle force constants (from 5000
> to 10.0).
>
> I ran a minimization (2500 steps) keeping restrained the heavy atoms of
> both protein and ligand and letting free water molecules and ions.
> Afterward a ran a min. (10000 steps) of the whole system (to min the
> system before running a MD):
>
> Initial XMIN minimisation of PknG-Adenine complex: complex, water and ions
> &cntrl
> imin=1,
> maxcyc=10000,
> ntmin=3,
> ntb=1,
> igb=0,
> ntr=0,
> cut=10,
> ntpr=10, ntwx=10, ntwr=1000
>
> The min. stopped at step 4230. There was no error message in the output
> file whereas i got a stdut error message:
>
> ERROR in load_lbfgs(): YS=0
>
> What does it mean?
>
> Thank you.
> valentina
>
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB
> Swiss Institute of Bioinformatics
> Klingelbergstrasse 61 | CH-4056 Basel |
>
> Phone: +41 61 267 15 80
>
>
> ________________________________________
> From: David A Case [case.biomaps.rutgers.edu]
> Sent: Saturday, May 17, 2014 2:46 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Analysis of minimization stage
>
> On Fri, May 16, 2014, Valentina Romano wrote:
>
> > Please find in attachment the files you need.
>
> It looks like you have dihedral angle force constants of 5000 or so (!)
> These
> are 2-3 orders of magnitude too big, and you will never be able to do
> molecular dynamics with such large forces.
>
> I think that in the past you seemed very worried about having non-planar
> groups, but I don't remember ever getting a clear answer to the question of
> whether you were seeing *small* or *large* deviations from planarity.
>
> In any event, go back to what Amber or gaff suggest for the magnitudes of
> these terms. They have been calibrated against vibrational frequencies of
> the
> out-of-plane modes. It is possible that minor adjustments might be needed
> (the
> original values were determined 30 years ago), but such changes would
> almost
> certainly be minor ones.
>
> ....dac
>
>
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--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
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Received on Tue May 20 2014 - 07:00:05 PDT
