Is it possible to visualize the optimized structure? Maybe some
minimization steps are necessary to remove strains in the docking pose.
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 - 15:30:03 PDT
