Thanks, it works now! Can I also set the PBradii in cpptraj? Because every
time it writes the closest.complex.prmtop file I have to change them using
parmed.
On 23 September 2016 at 21:45, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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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> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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
>
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
======================================================================
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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Received on Sat Sep 24 2016 - 17:30:03 PDT
