On Fri, Mar 17, 2017 at 3:19 PM, pengfei li <ldsoar1990.gmail.com> wrote:
> Hi everyone,
>
> I have a quick question about the distance criteria in AMBER mask.
>
> For the following representation:
>
> [(:5<:3.0)&:WAT]
>
> Does “:1-5<:3.0” mean the collection of residues for each has at least an
> atom within 3 angstrom of any atom of residues 1 to 5?
Yes. But note that the mask you have is just full residues in which at
least one atom is within 3 angstroms of any atom in residue 5. The &:WAT
means it also has to be in a WAT residue. See
http://parmed.github.io/ParmEd/html/amber.html#amber-mask-syntax for a more
detailed description.
HTH,
Jason
--
Jason M. Swails
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Received on Fri Mar 17 2017 - 13:00:04 PDT
