Daniel,
In the trajectory that I want to find the closest water to the COM there is
no crystal ligand, only protein and waters. Since in the <mask> I cannot
have the coordinates of the COM, then the only alternative I could think is
to find the closest protein residue to the crystal ligand and use this to
define the restraints in restraintmask. However, the "closest" command find
only closest waters, not closest protein residues. Is there any tweak to
allow that, like using the "solvent" command to redefine the solvent atoms
to be protein atoms?
best
Thomas
On 31 March 2017 at 18:24, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Finding the closest water to the COM of the ligand can be done with
> the 'closest' command in cpptraj:
>
> closest 1 <mask> out closest.dat first
>
> should get you what you want.
>
> -Dan
>
>
> On Fri, Mar 31, 2017 at 11:44 AM, Thomas Evangelidis <tevang3.gmail.com>
> wrote:
> > Hi Daniel,
> >
> > I want to simulate the apo form of a protein but there is a crystal
> > structure with ligand only. Since I also want to restrain all atoms apart
> > from those in the proximity of the ligand (including waters), I
> calculated
> > the COM of the crystal ligand and wanted to find all residues within 8 A.
> > Since passing coordinates in the restraint mask is not possible, finding
> > the closest water to the COM of the ligand is the only possible
> alternative
> > I could think of. Is this feasible with any other amber tool?
> >
> > Thanks,
> > Thomas
> >
> > Dne 31. 3. 2017 17:15 napsal uživatel "Daniel Roe" <
> daniel.r.roe.gmail.com>:
> >
> >> There aren't any commands which allow you to calculate the distance to
> >> specified coordinates. Probably the closest you could currently get to
> >> this in cpptraj would be to center your system on that point via
> >> 'center point <X> <Y> <Z>', then use 'distance <mask> <mask2>', where
> >> <mask> is your atom (or atoms) of interest and <mask2> is everything -
> >> this way <mask2> ends up centered on your point. Does that make sense?
> >> It sounds like interesting functionality to add to the 'distance'
> >> command. May also be useful to add this in general to things like
> >> 'closest' - I'll have to think about this.
> >>
> >> This all becomes much easier if you can define the point in terms of
> >> other atoms. Any reason you can't? If you describe in more detail what
> >> you're trying to do maybe I can think of another command that might
> >> help.
> >>
> >> -Dan
> >>
> >>
> >> On Fri, Mar 31, 2017 at 10:54 AM, Thomas Evangelidis <tevang3.gmail.com
> >
> >> wrote:
> >> > Thanks Hannes!
> >> >
> >> > Alternatively I could just find the closest water oxygen (that could
> work
> >> > for restarts too) and use that instead of the coordinates in the
> >> > restraintmask. Is this possible with cpptraj? I know that the
> "distance"
> >> > command calculates the distance between the COM of two selections, it
> >> > doesn't return the closest atoms to a point.
> >> >
> >> > best
> >> > Thomas
> >> >
> >> >
> >> > On 31 March 2017 at 15:35, Hannes Loeffler <
> Hannes.Loeffler.stfc.ac.uk>
> >> > wrote:
> >> >>
> >> >> Hi Thomas,
> >> >>
> >> >> On Fri, 31 Mar 2017 15:13:37 +0200
> >> >> Thomas Evangelidis <tevang3.gmail.com> wrote:
> >> >>
> >> >> > Is it possible to have coordinates in the restraint mask? For
> example
> >> >> > I want to restrain all atoms that are within 8 Angstroms from a
> point
> >> >> > in 3D space:
> >> >> >
> >> >> > restraintmask="! ( ( -13.5541 3.4173 15.1382 ) <: 8.0) )"
> >> >>
> >> >> I think you would need to do this with an actual atom at those
> >> >> coordinates (maybe even introduce a dummy atom if really necessary).
> >> >> And this will be only static that is the mask would be only computed
> >> >> once at the start of the simulations, so you would have to think what
> >> >> you want to do in case of restarts.
> >> >>
> >> >>
> >> >> Cheers,
> >> >> Hannes.
> >> >>
> >> >>
> >> >> _______________________________________________
> >> >> 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/
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> -------------------------
> >> 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
> >>
> > _______________________________________________
> > 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/
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Received on Sun Apr 02 2017 - 09:30:02 PDT
