Re: [AMBER] Question about addtobox

From: David Cerutti <>
Date: Thu, 9 Jan 2020 09:52:13 -0500

The -P slot is described by the arguments list obtained by running the
program with no arguments. It is there to define the upper limit of
protein atoms, so if there is already solvent you are happy with then
supply -P as the number of atoms to apply the -RP safety boundary against.
All other atoms it finds will be assumed "solvent" and get the -RW safety


On Thu, Jan 9, 2020 at 9:11 AM David Case <> wrote:

> On Thu, Jan 09, 2020, Petro wrote:
> >I believe this option is for the case when hydration is done iteratively.
> >And you have to add waters to a PDB with waters from previous run.
> I've done that sort of thing, or have added waters when
> "crystallographic" waters are already present. I stopped using the -P
> option years ago, and have never encountered any problems. (cc-ing
> again to Dave Cerutti for perspective here.)
> ....dac
> p.s: figuring out what number to put in the -P slot is a pain anyway, so
> it would be great if that task could be taken care of by the program.
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Received on Thu Jan 09 2020 - 07:00:01 PST
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