Thanks for the help dan. I was using ambertools 13, which is patched to the
latest version.
I tried the command as you suggested:
vector center :1-68.N,CA,C,O out check2.dat
and it gives identical results to
vector v0 center :1-68.N,CA,C,O :1-68.N,CA,C,O out prot_COM.dat
As you have confirmed that the first 3 numbers are the COM, I think it
should be ok. Thanks again for your help!
On Tue, Apr 7, 2015 at 4:30 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
> > ########################################
> > _______________________________________________
> > AMBER mailing list
> > 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 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Apr 07 2015 - 09:00:04 PDT
