AMBER Archive (2003)

Subject: AMBER: question about quasih?

From: Lishan Yao (yaolisha_at_pilot.msu.edu)
Date: Fri Jul 18 2003 - 17:15:32 CDT

Hi there:
   I have two questions about quasih program. The first one is: I run MD
for a ligand which has 23 atoms. I try to use quasih to get the
frequencies. If I put nmode less than around 30, it works fine. But when
it goes to 50 or even greater, it dies. This is the information I get
from the output:
Using 250 coordinate sets from 1 through 250
| Time to construct A: 0.03
dsaupd returns: -3
| Time for dsaupd : 0.00

And this is the command I use:
quasih -natom 23 -f 2 -m 969_mass -x xyz -v vec -nmode 60 -first 1 -last
250 < dhna_hp_1a.crd > 1a.out

Another question is: when I read the manual about quasih, it is said
that I need to use ptraj to superimpose them first. Then I run ptraj and
use 'rms' command. I assume this command should superimpose snapshots,
but I am not sure. Any suggestion?

Thanks in advance.

Sincerely
Lishan 

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

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