From: Jason Swails <>
Date: Fri, 26 Jul 2013 15:36:30 -0400

On Fri, Jul 26, 2013 at 10:39 AM, Hunter Brown <>wrote:

> requires three (usually four I think) prmtop files. The best way
> to prepare those is in LEaP. If I recall, the manual, and MMPB(GB)SA
> tutorial describe the usage quite nicely. If I recall correctly, an the
> MDCRD does not (and indeed should not?) need to be stripped of waters.

You can either have strip waters for you (in which case, you must
provide a solvated prmtop file via the -sp flag). Or you can strip it
beforehand (in which case, the solvated prmtop file must be omitted).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Jul 26 2013 - 13:00:08 PDT
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