From: Chris Harrison (charris5_at_gmail.com)
Date: Thu Oct 14 2010 - 17:28:22 CDT
TMDFile = target structure
TMD is active during MD. It is not a minimization method. You could
perhaps try cooling your system to 0 and perform a TMD MD. That might
be as close to a "TMD minimization" as you would get. But this is not
the intended purpose for the method, so "buyer beware."
On Thu, Oct 14, 2010 at 5:22 PM, <matziast_at_med.uth.gr> wrote:
> I try to write a script in order to do targeted molecular dynamics, but I do not
> understand some things:
> the TMDFile must be the initial pdb or the pdb that refers to the target
> structure(final structure)?
> Also, this segment will be part of a minimization script, how can I run it?
> Thank you in advance.
-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
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