In addition to what Jason mentioned, you may want to check out the
section in the Amber 14 manual that covers Amber atom mask selection
syntax (28.2.3). There is even a subsection that focuses on
distance-based masks.
-Dan
On Wed, Feb 25, 2015 at 6:17 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, Feb 25, 2015 at 7:36 AM, Alessandra Lacetera <
> alessandra.lacetera.gmail.com> wrote:
>
>> Thank you Daniel, more or less it was what I was searching for.
>>
>> The bad thing is that it finds also intramolecular distances and waters (I
>> will use grep command to take what I need).
>>
>> It would be great to have the possibility to specify both masks.
>>
>> E.G. mask "(:5 <:3.0 :1-4)", where :1-4 is the protein and :5 the ligands
>>
>
> You can almost certainly do this using the binary operators. What exactly
> are you trying to select? All residues containing an atom within 3
> angstroms of the ligand and protein? Do that with:
>
> "(:1-5 < :3)"
>
> All protein residues within 3 angstroms of the ligand? Do that with:
>
> "(:5 < :3.0) & :1-4"
>
> All protein atoms PLUS any other atoms within 3 angstroms of the ligand?
> Do that with:
>
> "(:5 < :3.0) | :1-4"
>
> And so on. The mask syntax is incredibly flexible, but admittedly somewhat
> opaque.
>
> Hope this helps,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Feb 25 2015 - 07:00:03 PST
