If you want to use prmtop file for your simulation or for energy
calculation, you should use tleap or ParmEd.
cpptraj is more like trajectory analysis.
Hai
On Sat, Sep 24, 2016 at 8:14 PM, Thomas Evangelidis <tevang3.gmail.com>
wrote:
> 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/
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > 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
> > AMBER.ambermd.org
> > 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/
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Sep 24 2016 - 23:30:03 PDT
