On Wed, 2014-03-05 at 15:53 +0530, DEBOSTUTI GHOSHDASTIDAR wrote:
> Dear Amber Users
>
>
> I need help with a basic restrained A-DNA simulation in water. I generated
> an A-DNA with a particular sequence using the 'nab' program. To minimize
> the DNA, I used torsional restraints for some of the sugar and backbone
> dihedrals and carried out a minimization in water. However, the minimized
> structure was no longer an A-DNA and the final restraints printed in the
> mdout file show severe penalties and great deviations from the desired
> angles.
Do you know that your restraints are correct to begin with? I would
suggest looking at the restraint energy on the first step of the
minimization and see how large the value is. If the restraint energy is
very large (as I expect it is), then your initial geometry is very far
away from at least one of your restraints. The huge forces resulting
from such a bad restraint would surely be enough to ruin your structure.
If that is not the case and your initial restraint energy is low, then I
would suggest looking for van der Waals clashes (the "checkoverlap"
command in ptraj or cpptraj will work nicely here). There has to be
some source of very large force (either from the restraints or van der
Waals clashes) that are destroying your structure.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Mar 05 2014 - 05:00:02 PST
