Hi,
No - as mentioned in the manual the only action command in which
distance-based masks update on a per-frame basis is the 'mask' command
- everything else uses the active reference structure. This is because
with a distance based mask you often have a changing number of atoms
selected each frame, which can make bookkeeping a nightmare.
What you probably want to do instead is use the 'closest' command so
that a certain fixed number of molecules is kept around your area of
interest prior to LIE. You can get an idea of how many waters to keep
with the 'watershell' command. See the manual for full details on
these commands.
Hope this helps,
-Dan
On Thu, Oct 6, 2016 at 2:12 AM, kurisaki
<kurisaki.ncube.human.nagoya-u.ac.jp> wrote:
> Dear Ambers,
>
> I would ask you for atom selection.
>
> I'm now focusing water molecules within 4 A from a solute.
> The atom selection is given as below, under usage of LIE in cpptraj.
>
> lie Lig (:298<:4.0)&:WAT :298&!(.CA,HA,C,N,H,O)
>
> But, I noticed that here is required to specify the reference structure,
> Which is not updated for each snapshot.
>
> I'm wondering whether I could update atom selection information
> by snapshot, but is it possible in the AmberTools14 or later?
>
> I'm glad if you answer this question.
>
> Thanks in advance,
> My best
>
> Ikuo KURISAKI
>
>
>
>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Oct 13 2016 - 07:00:03 PDT
