VMD-L Mailing List

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Mon May 11 2020 - 14:12:25 CDT

If it's stable, it sounds like it's reasonable for you. We've previously run zinc-coordinated states by introducing bonds with the zinc ion and checking that the geometry is maintained. This is safer because you know your ion won't fly away halfway through your simulation.

Best,
JC
________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of varun dewaker <varun_dewaker1986_at_REMOVE_yahoo.com>
Sent: Saturday, May 9, 2020 1:40 PM
To: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Regarding zinc parameters in CHARMM force field

Dear VMD users
I use NAMD for MD simulation. We parametrize the zinc ion or generate their psf and pdb file using parameters present in the top_all27_prot_na.inp, CHARMM force filed. The reference for this is “Zinc Binding in Proteins and Solution: A Simple but Accurate Nonbonded Representation” (Stote & Karplus, 1995). It uses a simple non-bonded model based on the combination of Lennard-Jones and electrostatic interactions. They mentioned that these parameter set permits different coordination geometries and ligand exchange for the zinc ion and can be employed effectively for both solution and protein simulations of zinc-containing systems.
During dynamics, the system (protein-ligand-zinc-water) runs properly and zinc remains at their position.
Is this method is not good? Needed your valuable suggestions/comments or justifications. Kindly participates.

Thanks

Regards,
Varun Kumar Dewaker
Research Fellow
QSAR & Molecular Modelling Lab
MPC Division (CSN-202)
CSIR- Central Drug Research Institute
Lucknow - 226031 (U.P), India