AMBER Archive (2006)

Subject: Re: AMBER: amber .off file format question

From: David A. Case (case_at_scripps.edu)
Date: Tue May 23 2006 - 01:21:33 CDT

On Tue, May 23, 2006, Ilyas Yildirim wrote:
>
> When only the charge is perturbed, the atom is seen as
> UNPERTURBED in xleap when the desc command is used. When the atom changes
> its TYPE, then it is seen as perturbed.

Hi Ilyas:

I hope you are transitioning to Amber 9, where there are no more "perturbed
prmtop files", or any of the difficulties in distinguishing between charge
changes and atom type changes, etc.

Of course, there are probably some new problems (esp. with SHAKE, as you
know), but in the long run, things should be much simpler.

Wei: it should not be necessary for gleap to support the old perturbation
behavior.

...regards...dac

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