AMBER Archive (2007)

Subject: Re: AMBER: ptraj and quasi harmonic analysis

From: David A. Case (case_at_scripps.edu)
Date: Fri Apr 20 2007 - 10:23:34 CDT

On Thu, Apr 19, 2007, Hans Lee wrote:
>
>
> Yes. I have 200 frames for complex, receptor and ligand respectively.
> Instead of running separate trajectories, simulation was carried out on
> the complex only. Snapshots for receptor and ligand were extracted from
> the complex trajectories. I am not sure how the results will improve if
> simulations were carried out on complex, receptor and ligand respectively.
> The structures were minimized before Matrix calculation.

First, 200 snapshots is way too few to see much of anything from quasiharmonic
analysis, and enormously too few to use to compute an entropy. Second, the
structures should not ordinarily be minimized prior to quasiharmonic analysis:
the idea is to help in understanding the nature of the thermal fluctuations
that take place.

...hope this helps...dac

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