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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Received on Tue May 20 2014 - 07:00:04 PDT
