AMBER Archive (2003)

Subject: Re: AMBER: Question about quasih analysis

From: David A. Case (case_at_scripps.edu)
Date: Mon Jul 28 2003 - 11:16:13 CDT

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?

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

I don't see where this limit is enforced. What is the error message (or
other behavior) if you ask for more than 3N/2 modes?

> 3. How the moments of inertia are calculated, from the average structure
> or from each structure then take an average?

>From the average structure.

..good luck...dac 

-- 

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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
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