Dear Bhat,
yesterday Vaibhav Dixit suggested to use mcpb.py for a similar case.
There is a detailed tutorial about this type of parameterization on the
Amber website.
Maybe you could also try out a simple non-bonded model for your ion.
(cf. the metal ion modeling tutorial on the Amber website).
Whether, however, the available parameters are suitable in your case,
you have to decide yourself, i.e. whether your coordination complex is
expected to be stable or just transient, and what your study is aiming
at. Perhaps test simulations would tell you more...
Best regards,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 28.10.2021 um 10:20 schrieb Bhat Zahoor:
> Dear Amber Community,
>
> I want to simulate protein ligand interaction wherein Ca2+ ion is in 8
> coordination geometry with protein and ligand.
>
> I am not sure about the forcefield parameters for the Ca2+ ion in this
> coordination geometry. Any sort of help shall be appreciated.
>
> Thank you in anticipation
> _______________________________________________
> 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 Thu Oct 28 2021 - 05:00:02 PDT
