AMBER Archive (2005)

Subject: Re: AMBER: amber file formats.

From: David A. Case (case_at_scripps.edu)
Date: Thu Oct 20 2005 - 16:32:29 CDT

On Fri, Oct 21, 2005, Shishir wrote:
>
> - what is the unit of force in Amber

kcal/mol-A.

> (btw, I am not
> convinced of your analogy here, pdf was never designed to be
> modifiable - it preserves author's intentions, machine dependent
> things.

For some simple things, hand-editing a prmtop file (or using the facilities in
ptraj) can work. You can change the box size, or modify some atom charge, or
strip out all waters, and so on. But more general modifcations directly to
prmtop file are not in general possible. For example, it would be nearly
impossible to decide to change residue 276 from alanine to valine. (At least,
I don't see how generic changes like that could be made.)

....dac

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