I need some advice about GB simulations of a protein-ligand complex with
Zn2+ ion. No matter which GB model I use, the aromatic pentameric ring
binds to the ion and becomes distorted, as shown in these photos:
https://dl.dropboxusercontent.com/u/48168252/ligand2.png
https://dl.dropboxusercontent.com/u/48168252/pentamer_ring.png
The frcmod of the ligand looks like this:
remark goes here
> MASS
> BOND
> n1-cc 536.50 1.311 same as ce-n1
> ANGLE
> n1-nd-cd 75.270 115.090 same as c2-n2-n1
> n1-cc-nc 75.888 118.985 Calculated with empirical approach
> n1-cc-h5 51.660 121.535 Calculated with empirical approach
> *nd-n1-cc 0.000 0.000 ATTN, need revision*
> DIHE
> IMPROPER
> c3-nc-cd-nd 1.1 180.0 2.0 Using default
> value
> h5-n1-cc-nc 1.1 180.0 2.0 Using default
> value
> NONBON
I don't think that the missing angle is the problem, neither the charges
because some ligands with the same ring do not bind to Zn2+ but still the
aromatic ring plane is distorted during the simulation. Do you believe than
the impropers are insufficient and I must add more? Has anyone observed the
same artifact in GB simulations?
Btw, why the radius of both Zn2+ and Mg2+ is 1.5 A. when measured in VMD?
Shouldn't they be different?
I would be grateful for any advice.
Thomas
--
======================================================================
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 - 04:30:03 PDT
