Hi,
I think you may need to change your input. I'm assuming you want to
keep waters that are within a certain distance (4.0 Ang in this case)
from residue 4. As stated in the manual, only the 'mask' command works
with distance-based masks on a frame-by-frame basis. The mask for
'strip' is evaluated once (based on the active reference). Also, you
may have a changing number of atoms based on this kind of selection,
which makes writing trajectory files difficult. I think the 'closest'
command is probably a better bet. First you can determine how many
waters are within 4.0 Angstroms of residue 4 in a single frame:
parm complex.prmtop
reference complex.prod_GB.nc 11
select (:LIG<:4.0)&:WAT.O
You'll get output that looks something like:
Selected 14 atoms.
Selected= 302 641 1274 1373 1661 3209 3287 3305 3368 3764 4196 4199 4202 4214>
Then you can use the 'closest' command to retain that number of waters
(maybe pad it by a couple) and write out that trajectory/do analysis
etc:
closest 16 :1 first outprefix closest
trajout complex.MMGBSA_GB.WAT4Ang.nc
See manual for full details. Hope this is something like what you want,
-Dan
On Fri, Sep 23, 2016 at 9:23 AM, Thomas Evangelidis <tevang3.gmail.com> wrote:
> Greetings,
>
> I want to strip the waters that are further than 4 Ang. from the ligand. I
> tried to do it with cpptraj like this:
>
> cpptraj complex.prmtop << EOF
> reference complex.prod_GB.nc lastframe
> trajin complex.prod_GB.nc 11 15
> mask "(:LIG >:4.0) & :WAT" maskout delWAT4Ang_mask.txt
> strip "(:LIG >:4.0) & :WAT" outprefix complex2
> trajout complex.MMGBSA_GB.WAT4Ang.nc
> go
> quit
> EOF
>
> But cpptraj strips all the waters and leaves only the ligand and the
> protein. What am I doing wrong?
>
> thanks,
> Thomas
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> Research Specialist
> CEITEC - Central European Institute of Technology
> Masaryk University
> Kamenice 5/A35/1S081,
> 62500 Brno, Czech Republic
>
> email: tevang.pharm.uoa.gr
>
> tevang3.gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
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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 Fri Sep 23 2016 - 13:00:02 PDT
