AMBER Archive (2003)

Subject: Re: AMBER: Question about quasih analysis

From: David A. Case (case_at_scripps.edu)
Date: Mon Jul 28 2003 - 13:37:20 CDT

On Mon, Jul 28, 2003, Lishan Yao wrote:

> > On Mon, Jul 28, 2003, Lishan Yao wrote:
> >
> > > I use quasih program to do the entropy calculation for
> > > 6-hydroxymethyl-7,8-dihydropterin.
> >
> > > 1, Those low frequencies are kind of too low. what kind of motion can
> > > have these low frequencies for a small organic molecule. When I use MP2
> > > to do the frequency analysis, I get totally different results.
> >
> > Did you use ptraj to remove overall translation and rotation before running
> > quasih?
> Yes, I think I did. This is what I did:

What you did looks OK to me. You should certainly look at the values in the
rms_to_average_frame.dat file: are they all quite small? You may also need
to visualize the md_nvt23_now_fit.crd trajectory to see if there are any
conformational transitions taking place, etc.

(Or maybe someone else on the list will spot a problem with the ptraj
scripts).

> >
> > > 2. The number of frequencies given by this program is less than or equal
> > > to 3N/2 (Is there any reason behind this?).

Change line 227 in quasih.f from

      ncv = 2*nev

to

      ncv = min( 2*nev, n )

and recompile. That should help; if so, I'll post a bugfix.

..regards...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. | home page:
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