VMD-L Mailing List

From: t.shivam_at_iitg.ernet.in
Date: Wed Feb 07 2018 - 10:11:39 CST

Dear vmdusers,

I am working on metal ion protein interaction, and i want to prepare the
initial structure of metal occupying the active site of the protein,

I am facing following issues:

1)I want to put the metal ion at the active site and i know the ligating
residues, but how to know the exact coordinates at which metal ion need to
be put.
*I know we can use a docking software to do this, but since i have no
experience with docking, i was wondering weather this can be done without
it also.

2)while creating psf do we need to create a separate segment for metal or
it will come under the same segment as all other atoms of protein.

3)Also if you can advice on an appropriate simulation protocol to be
followed for such system, as i will be using charm ff which has non-bonded
parameters for zinc, i need to restrain the metal at its position, scale
down the restrains gradually.
*I know i should ask the last question on the namd mailing list.

regards
shivam