[AMBER] energy minimum vs binding pose for charge calculation

From: Thomas Evangelidis <tevang3.gmail.com>
Date: Wed, 1 Nov 2017 15:45:32 +0100


I want to calculate AM1 charges and run MD simulations for hundreds of
molecules in batch mode. For some of them, SQM fails to converge and
returns this error:

QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.1893E+07 DeltaE = 0.1983E+00 DeltaP = 0.3701E-01
QMMM: Smallest DeltaE = 0.1041E-06 DeltaP = 0.9668E-04 Step = 98

One solution would be to increase the scfconv from 1.d-10 to 1.d-8 and grms_
tol from 0.0005 to 0.005 inside sqm.in file. Btw, is it possible to pass
these settings directly to Antechamber instead of amber16/bin/sqm?

The other option could be to pass energy minimized geometries to
antechamber. Currently, I pass the binding poses, which sometimes differ
substantially from the energy minimum. However, assuming that antechamber
finishes successfully, which charges would be better for simulating the
protein-ligand complex, those calculated using the energy minimum or those
calculated using the real binding pose of the ligand?

Thanks in advance.

Dr Thomas Evangelidis
Post-doctoral Researcher
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/2S049,
62500 Brno, Czech Republic
email: tevang.pharm.uoa.gr
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Wed Nov 01 2017 - 08:00:03 PDT
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