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.
> >>
> >>
> >> _______________________________________________
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> >> 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
>
> _______________________________________________
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>
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Received on Fri Mar 31 2017 - 09:00:03 PDT
