Quoting NI AI <aini.UMDNJ.EDU>:
> Dear Dr. Cheatham,
>
> Thank you very much for your answer! I striped water and counter ions and
> used modified script. The minimization went through. However, this
> minimization is done in vaccum since I don't know how to put water and ions
> back to the system. Do I need to read in average.pdb to xleap and prepare
> another .top and .crd file for minimization? or you have different way to do
>
> that?
My experience with average structures is limited to preparation of several
presentation graphics to describe key interactions in a ligand/protein complex I
am working on.
For this work, minimization of average.pdb, simply and quickly in vacuum, by
creating a new .top and .crd worked out fine (protons had normal positions, bond
lengths, etc). Of course, you'll want to look at what you get :)
Chris
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Received on Fri Jul 02 2004 - 18:53:00 PDT
