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.
On Fri, Sep 16, 2016 at 7:03 AM, Thomas Evangelidis <tevang3.gmail.com>
wrote:
> 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/
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 16 2016 - 05:00:02 PDT
