Re: can someone comment?

From: Cesar Avila (
Date: Sat Apr 07 2007 - 11:57:49 CDT

Dear Harish,
I would strongly recommend you to check CHARMM's forum for how to deal
with Zinc ions. There is a lot of ongoing work on how to properly treat
protein-bound zinc atoms on molecular mechanics forcefields. Keep in mind
that we are dealing with a simplified model for the system. Using only
nonbonded interactions to describe Zn's behaviour lead's to bad
Cesar Avila

> Hi all,
> I have read suggestions at several places in mailing archive about
> minimizing the system till Gradient Tolerance reaches in single
> digits or below 1.0 etc. Further, we all know that energy minization
> is done to remove any bad VDW contacts which may lead to high forces
> during MD.
> Using the gradient tolerance criterion, i subjected my system to 1000
> steps of steepest descents and plotting Total and VDW energy shows a
> continued decrease in total energy which is ofcourse desired but an
> increase in VDW energy after an initial decrease. Is it wise to leave the
> system at high VDW energy even though gradient tolerance is nearly to
> ~4.0. Any comments on this are highly appreciated.
> Further, Should we keep the essential ions such as "ZN" or other found in
> most proteins fixed because minimization distorts the ligand geometry
> most of the time--atleast in my case?
> Regards
> Harish
> -------------------------------------------------
> Harish Vashisth (Ph.D Candidate)
> CAT-361,Chemical & Biological Engg.
> Drexel University, Philadelphia, PA
> office: 215-895-5823

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