Thanks Daniel,
That really helped a lot.
On Tue, Feb 19, 2013 at 7:25 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> This could potentially be done in current versions of ptraj/cpptraj
> with a 'vector' command; the origin coordinates (2nd set of 3) should
> be the COM of whatever mask you set. For example, using the input:
>
> vector v0 :5 :5 out v5.out
>
> the output will look like:
>
> # FORMAT: frame vx vy vz cx cy cz cx+vx cy+vy cz+vz
> # FORMAT where v? is vector, c? is center of mass...
> 1 0.0000 0.0000 0.0000 -3.0022 2.7312 -2.5133 -3.0022
> 2.7312 -2.5133
>
> where the second set of 3 numbers (as well as the third) are the XYZ
> coords of the center of mass of residue 5.
>
> In the upcoming release of cpptraj there is a dedicated command for this.
>
> -Dan
>
> On Tue, Feb 19, 2013 at 5:11 AM, HM <scienceamber.gmail.com> wrote:
> > Hi All,
> > I was just wondering how can I dump the center of mass coordinates for a
> > particular protein domain in a text file. Is there any option in ptraj or
> > cpptraj for that..
> >
> > Thanks,
> > HM
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Feb 28 2013 - 04:00:03 PST
