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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--
-------------------------
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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Received on Tue Feb 19 2013 - 10:30:03 PST
