Re: [AMBER] Question about addtobox

From: David Case <>
Date: Wed, 8 Jan 2020 15:22:21 +0000

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


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Received on Wed Jan 08 2020 - 07:30:02 PST
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