I did explicit solvent MD and still the ion distorts the ring. So the
problem is with the ligand/Zn force field. What should I look next? The
impropers?
On 16 September 2016 at 13:41, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> do you know this is GB and not the ligand/Zn force field? meaning does it
> work fine in explicit water? I don't know which GB model you are using, but
> GB uses parameters like intrinsic radii and especially some descreening
> parameters that are optimized but may not be present for Zn. Try to
> separate whether it's GB or the force field-- could be either.
>
>
>
--
======================================================================
Thomas Evangelidis
Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
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 Fri Sep 16 2016 - 09:30:02 PDT
