Hi,
First, which version of cpptraj are you using? The 'vector center'
command takes only one atom mask, so
> vector v0 center :1-68.N,CA,C,O :1-68.N,CA,C,O out prot_COM.dat
with two masks should give an error.
On Tue, Apr 7, 2015 at 8:51 AM, George Green <soyo.green.gmail.com> wrote:
> The command seems to work and I get the output included below. However,
> from looking at the mailing list, the COM is meant to be the second set of
> three numbers. see http://archive.ambermd.org/201302/0377.html
The post is from a time when the 'center' functionality of the
'vector' command didn't exist, and refers to older versions of code.
This just tells you how to use the older form of the command to obtain
the center of mass of a selection. Now you can just use 'vector
center', in which the first 3 numbers are the center of mass of the
selection.
Unless you have a specific reason, I recommend using the latest
version of the Amber manual as a reference instead of older posts. For
example, from the Amber 14 manual on the cpptraj 'vector' command
(Section '28.11.3 vector'):
*center* Store the center of mass of atoms in *<mask1>*. The reference
point is the origin (0.0, 0.0, 0.0).
Hope this helps,
-Dan
>
> However, the output is not the same as that in the link above. Not sure if
> I have fully understood the vector command properly. If someone could
> hopefully offer some guidance that would be great!
>
> ########################################
> #Frame v0
> 1 34.3814 32.3427 27.5217 0.0000 0.0000 0.0000
> 2 34.3852 32.3313 27.5320 0.0000 0.0000 0.0000
> 3 34.3806 32.3322 27.5277 0.0000 0.0000 0.0000
> 4 34.3855 32.3349 27.5257 0.0000 0.0000 0.0000
> 5 34.3868 32.3368 27.5282 0.0000 0.0000 0.0000
> 6 34.3835 32.3379 27.5248 0.0000 0.0000 0.0000
> 7 34.3799 32.3291 27.5326 0.0000 0.0000 0.0000
> 8 34.3786 32.3375 27.5250 0.0000 0.0000 0.0000
> 9 34.3779 32.3353 27.5360 0.0000 0.0000 0.0000
> ########################################
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Apr 07 2015 - 09:00:03 PDT
