Hi,
Thank you for again for your advice.
> First: if you reply to a digest mail (that contains lots of messages),
> please
> delete all the non-relevant material. Otherwise, it is very hard to even
> find your question.
>
Sorry for that, I will take care of that while posting the queries again.
>
> > > > Coordinate resetting (SHAKE) cannot be accomplished,
> > > > deviation is too large
> > > > NITER, NIT, LL, I and J are : 0 2 392 803 804
> > >
> > > The problem is at atoms 803 and 804. Check your structure carefully at
> > > that point.
> > >
> >
> > Thank you for your response. I looked at the pdb file and atoms 803 and
> 804
> > are O and H, respectively of a water molecule.
>
> So: did you "check the structure carefully" in that region? Is there
> anything
> special about that water? Have you visualized its interactions with the
> rest
> of your system?
>
Yes, I checked and I found that the O (803) and H (804) are bonded to one
of the protein residues. I also checked the density.rst structure in tleap
using the check command and I found the same problem with three other water
molecules (which were not shown as an error while performing
equilibration).
> check com
Checking 'com'....
Warning: Close contact of 1.490077 angstroms between .R<WAT 2455>.A<H1 2>
and .R<WAT 2470>.A<O 1>
Warning: Close contact of 1.466524 angstroms between .R<WAT 16301>.A<H1 2>
and .R<WAT 17044>.A<O 1>
Warning: Close contact of 1.442608 angstroms between .R<WAT 16436>.A<H2 3>
and .R<WAT 16652>.A<H2 3>
Checking parameters for unit 'com'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 3
Unit is OK.
So what could be the problem? Am I not minimizing the solute enough. My
current settings are:
Minimization of waters
&cntrl
imin=1, maxcyc=10000, (*in tutorial maxcyc was 5000*)
ncyc=5000, ntb=1, (*in tutorial ncyc was 3000*)
cut=12, ntpr=5,
ntr=1,
restraint_wt=2.0
&end
Group input for restrained atoms
100.0
RES 1 535
END
END
I changed the values for maxcyc and ncyc in my settings and rest parameters
were same.
Or the box size might be small?? I used 12.0 and closeness 0.78, as
mentioned in the tutorial.
Regards
BM
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jun 26 2016 - 18:30:03 PDT
