On Wed, Mar 03, 2021, Ramanathan Rajesh wrote:
>*vlimit exceeded for step 38683;
Is this the first time you saw a vlimit error? You should visualize the
trajectory up to that point, and see if there are any bad contacts between
the ligand and the quadruplex. Is the temperature stable?
It would help to know how you created the force field for the ligand.
>large NITER, NIT, LL, I and J are : 0 4 281 882 891
Look in particular at atoms 882 and 891, and their immdiate surroundings.
You may want to run a shorter simulation that stops shortly before the
error, and look at the final structure from the restart file.
>I want to know if such procedure can be followed that is without a docked
>structure performing a simulation using a gaussian optimized structure of
>ligand by manually placing it over a guanine residue in the G-quadruplex.
It's possible that the problem arose from a poor initial placement, but
since you have run 38,000 steps before encountering a problem, it seems more
likely that the system is allowing a bad contact somewhere.
....dac
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Received on Wed Mar 03 2021 - 06:00:07 PST
