Re: can someone comment?

From: hl332_at_drexel.edu
Date: Sat Apr 07 2007 - 17:36:12 CDT

Hi Cesar,
   Thanks a lot for your advice. I would look there for sure. If you have got the link of some particular thread on CHARMM which can save me a little search effort, it would do great otherwise i can find it out. Also, share some ideas about my first problem (minimization) if you have got something?

Thanks and regards
Harish

-------------------------------------------------
Harish Vashisth (Ph.D Candidate)
CAT-361,Chemical & Biological Engg.
Drexel University, Philadelphia, PA
office: 215-895-5823

----- Original Message -----
From: Cesar Avila <cavila_at_fbqf.unt.edu.ar>
Date: Saturday, April 7, 2007 12:57 pm
Subject: Re: namd-l: can someone comment?

> 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
> treatprotein-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
> geometries.
> Regards
> 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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