AMBER Archive (2003)

Subject: Re: AMBER: Question about quasih analysis

From: Lishan Yao (yaolisha_at_pilot.msu.edu)
Date: Mon Jul 28 2003 - 12:30:26 CDT

On Mon, 2003-07-28 at 12:16, David A. Case 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:
1, remove water, and get average structure for the compound.
trajin md_nvt2.crd 1 250
trajin md_nvt3.crd 1 250
strip :~1
center mass origin
rms first mass out rms_to_first_frame.dat
average avg.pdb pdb
trajout md_nvt23_now.crd
go

2. overlay all the snapshots to the average structure
trajin md_nvt23_now.crd 1 500
reference avg.pdb
rms reference mass out rms_to_average_frame.dat
trajout md_nvt23_now_fit.crd
go
Then I use this trajectory to do the frequency analysis.
>
> > 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?
I got this 3N/2 information from the response of my question "question
about quasih?" posted several weeks ago. I tried it. My compound has 23
atoms. When I use 34(3*23/2), it works fine. When I use 35, I got:

sing 500 coordinate sets from 1 through 500
| Time to construct A: 0.08
dsaupd returns: -3
| Time for dsaupd : 0.00

>
> > 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 

-- 
Lishan Yao <yaolisha_at_pilot.msu.edu>
MSU

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