AMBER Archive (2007)

Subject: Re: AMBER: entropy with ptraj

From: David A. Case (case_at_scripps.edu)
Date: Mon Oct 08 2007 - 08:47:57 CDT

On Mon, Oct 08, 2007, Marius Retegan wrote:

> I'm trying to use ptraj to calculate the entropy for o small ligand
> from a dcd trajectory.
> I've used the following input
> ================================
> trajin inhibitor.dcd
> rms first *
> matrix mwcovar name mwcvmat
> analyze matrix mwcvmat thermo reduce
> go
> ================================
> If I align the structures using rms first * I get high energy for the
> last 6 frequencies

This is correct (i.e. what you should expect). In principal component
analysis, there is no net rotational or translational motion (since you
aligned the frames), and this appears as a very large force constant for
these modes.

...hope this helps....dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  skype:                 dacase
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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