Hi,
As stated in the manual, for most actions distance-based masks work
based off of a reference structure and do not update frame-by-frame
(the exception being the 'mask' action). However, using 'strip' with a
distance-based mask is still not what you want because the number of
waters kept will probably fluctuate from frame to frame (meaning no
one topology would work for this). Instead, you probably want to use
the 'closest' action which will keep a fixed number of waters close to
your solute. Use the 'watershell' command first to determine how many
waters you will need to keep (probably best to keep at least two
shells if you want to look at water interactions later on). See the
manual for details on these commands.
Hope this helps,
-Dan
On Wed, Mar 9, 2016 at 8:02 AM, windy <chxp_moon.163.com> wrote:
> Hi,
>
> Everyone.
>
> I have a lot of trajectories and short for the hard disk space. So I managed to reduce the trajectory file size.
>
> Using the NETCDF format is the first choice.
>
> Further more, for that my simulation is just a water environment, I can strip the waters to reduce the trajectories file size.
>
> However, I am not sure I would analysis the interaction between the water and some residues (like residue his, asp) in the future. So I used the a script to strip the water which the distance long than the protein residues (4A). The script is show as here:
>
> trajin convet1.nc
> autoimage
> reference init.pdb
> strip "(:1-267>:4)&(:WAT)" outprefix sp1
> trajout sp1.nc
>
> The scripts no working. It remove all the waters and do not maintain the water in the protein. I change the distance 4 from 1 to 10, no working too (:1-267 is my protein).
>
> Anyone have a good idea? Thanks...
>
> Chen.
>
>
>
>
>
>
>
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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 Wed Mar 09 2016 - 08:00:04 PST
