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
--
==================================================================
David A. Case | e-mail: case.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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Received on Mon Jul 28 2003 - 17:53:01 PDT
