Hi,
On Tue, Jun 21, 2016 at 3:27 AM, Alessandro Contini
<alessandro.contini.unimi.it> wrote:
> Since I've read in the
> manual that distance based actions do not update on a per frame based, I
> was trying both strip and mask commands but without success. Does
> anybody can point me toward a way of doing this?
Without knowing specifically what you tried, I can only offer general
suggestions. The main issue with having a distance-based mask during
trajectory processing is that the number of things selected will
change, so things like writing to a trajectory format can become
problematic. The way cpptraj currently does what you want is via the
'mask' command, which allows you to output a PDB or Mol2 file for each
frame based on whatever mask you give it. For example, to select all
water residues (named WAT) within 3.0 Angstroms of residue 5 and write
them to Mol2 files:
mask (:5<:3.0)&:WAT maskmol2 mask.mol2
Hope this helps,
-Dan
>
> Thank you and best regards
>
> Alessandro
>
> --
> Alessandro Contini, PhD
> Dipartimento di Scienze Farmaceutiche
> Sezione di Chimica Generale e Organica "A. Marchesini"
> Via Venezian, 21 20133 Milano
> tel. +390250314480
> e-mail alessandro.contini.unimi.it
> skype alessandrocontini
>
> http://www.scopus.com/authid/detail.url?authorId=7003441091
> http://orcid.org/0000-0002-4394-8956
> http://www.researcherid.com/rid/F-5064-2012
>
>
>
>
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--
-------------------------
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 Tue Jun 21 2016 - 07:30:02 PDT
