Re: [AMBER] Question about addtobox

From: Petro <>
Date: Thu, 9 Jan 2020 00:19:41 +0100

Thanks Dave.
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.

On Wed, Jan 8, 2020, 16:22 David Case <> wrote:

> On Wed, Jan 08, 2020, Petro wrote:
> >I have a question about addtobox program.
> >In the tutorial on the Amber website a PDB without hydrogen's used. Can it
> >be used on pdbs with hydrogens or they have to be removed. Does the
> program
> >takes into account hydrogen's in pdb? Shall they be counted in number
> >supplied by P parameter?
> AddToBox doesn't do anything special with hydrogens: they can be there,
> no not be there -- it's up to you.
> >What are the consequences is number of protein atoms supplied by parameter
> >P is smaller then actual number?
> I think the P option is not really needed at all (cc-ing to Dave Cerutti).
> The program figures out how many atoms are there by itself. (Dave: is
> there some use case for having P be smaller than the actual number of
> atoms?)
> ....dac
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Received on Wed Jan 08 2020 - 15:30:02 PST
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