Thank you.
Schrodinger offers a modules named "QM-Polarized Ligand Docking", which
essentially selects the best docking pose by generating docking poses, then
calculating charges for each pose using the pose coordinates without
optimizing the geometry, then redocking the ligands and calculating the
docking score using the new charges. They claim to obtain superior results
in terms of correct pose prediction. In my case the docking pose is known,
so I was wondering if calculating AM1 charges by skipping the geometry
optimization will, at least implicitly and in some extent, capture the
polarization effect on the ligand induced by receptor-binding, and thus
improve MD results.
On 1 November 2017 at 18:56, David A Case <david.case.rutgers.edu> wrote:
> On Wed, Nov 01, 2017, Thomas Evangelidis wrote:
> >
> > QMMM: 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?
>
> Yes: use the "-ek" parameter in antechamber, which will put that
> information
> in the sqm.in file. See Notes 6 and 7 of Section 15.2 of the Reference
> Manual.
>
> >
> > 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?
>
> If it makes a difference, you might want to consider multi-conformer fits.
> Note that you can turn off minimization via the "-ek" flag, if you wish
> to use the input geometry.
>
> ....dac
>
>
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>
--
======================================================================
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
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Wed Nov 01 2017 - 11:30:03 PDT
