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.
>> >>
>> >>
>> >> _______________________________________________
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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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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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
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Received on Fri Mar 31 2017 - 09:30:02 PDT
