From: varun dewaker (varun_dewaker1986_at_yahoo.com)
Date: Tue May 05 2020 - 00:26:12 CDT
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.
Regards,Varun Kumar DewakerResearch FellowQSAR & Molecular Modelling LabMPC Division (CSN-202)CSIR- Central Drug Research InstituteLucknow - 226031 (U.P), India
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