[AMBER] Simulation of optimized ligand without docking

From: Ramanathan Rajesh <ramanathanrajesh30986.gmail.com>
Date: Wed, 3 Mar 2021 17:49:38 +0530

Dear all
I am working with G-quadruplex. I wanted to know if it is possible to
directly place the optimized structure of the ligand above a desired
guanine and run a MD simulation without docking(although there are some
overlap of ligand with the quadruplex).
I had tried this but the heating stage is not getting completed due to the
following error

*vlimit exceeded for step 38683; vmax = 34.0245vlimit exceeded for
step 38684; vmax = 38.2067vlimit exceeded for step 38685; vmax =
   24.133vlimit exceeded for step 38686; vmax = 4184.6232
 Coordinate resetting (SHAKE) cannot be accomplished, deviation is too
large NITER, NIT, LL, I and J are : 0 4 281 882 891
   Note: This is usually a symptom of some deeper problem with the
energetics of the system*

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.
Thanking you in advance
Ramanathan R
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Received on Wed Mar 03 2021 - 04:30:02 PST
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