AMBER Archive (2003)

Subject: AMBER: How to use quasih?

From: A. Hungie (hungie01_at_hotmail.com)
Date: Thu Dec 11 2003 - 10:12:23 CST

Dear All,

I am going to calculate vibration frequency of DNA using quasih program
(from AMBER 6 package). User manual could not make me clear how to use it
and therefore I would ask for your suggestions.

My system contains 800 atoms of DNA, 20 Na+ ions and 10500 atoms of water
molecules (total 11320 atoms). The 7 ps MD trajectory stored coordinates of
all atoms every 2 fs (total 3500 snapshots). The trajectory contains only
coordinates, without velocity. I would like to calculate vibration frequency
of only DNA. Someone has suggested me to run trajectory through PTRAJ and
average DNA structure. Therefore, in file "average.pdb" contains only DNA
without solvent and counter-ions. My questions are as follow.

1. to run quasih, it should be
    quasih -nat # -f # -x xyz [-novec| -v vecs] -first # -last # -lastvec
For number of atoms "nat", what should I put? 800 or 11320?

2. If nat=800, do I have to extract coordinates of DNA from trajectory
(delete coordinates of solvent)? If I have to delete coord of solvent,
should I also delete size of simulation box inserted between each snapshot?

3. Do trajectory storing coords every 2fs and trajectory storing coords
every 500 fs give the same vibration frequency?

Thank you very much for your suggestions in advance.

Best Regards,
Hungie

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