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 ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu