Re: AMBER: General AMBER questions

From: David A. Case <>
Date: Wed, 18 Jul 2007 16:12:34 -0700

On Tue, Jul 17, 2007, Lili Peng wrote:
> 1. How do we extract a file of the output data? I have Googled this
> problem, and I came up with "ambpdb" and "ptraj" - is this the right
> direction?

It's not clear what sort of "output data" you want. The tutorials (see,
esp. B1) illustrate common ways to analyze data from simulations.

> 3. Is there a way to determine the timescale for an energy minimization run?

Minimization doesn't have a "timescale" in the way the molecular dynamics
does. It is a static sort of conformational analysis.

> 4. From reading literature, I've noticed that a lot of authors use RES to
> calculate RESP charges for molecules. Is it always necessary to do this
> prior to an MD simulation, or energy minimization?

This is generally needed only if you are undertaking studies on non-standard
molecules, for which no charges are available already. I'd recommend getting
comfortable with standard simulations before trying more general things.
Then, see tutorial B4 for a road-map of one way to proceed.


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Received on Sun Jul 22 2007 - 06:07:18 PDT
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