On Fri, Jun 28, 2013 at 9:50 PM, Hongyi WU <why0713.sjtu.edu.cn> wrote:
> I'm afraid "average" do a totally different job.
>
> The description for "avgcoord" is:
> "For each frame, calculate the average X, Y, and Z coordinates over all
> atoms in <mask>"
> But "average" is also time-averaged as I believe.
>
> Daniel tells me that "avgcoord" has been replaced by "vector center"
> command:
> vector center <mask> out <filename> [magnitude]
>
Indeed, Dan's answer is the appropriate one ;). I guess I should RTFM when
I'm unfamiliar with a command rather than try to guess based on its name.
It was indeed right there in the cpptraj section of the manual...
Thanks Dan for the correction and apologies for the noise.
All the best,
Jason
>
> Anyway, I would like to thank you for your help. ^_^
>
> -----ÓʼþÔ¼þ-----
> ·¢¼þÈË: Jason Swails [mailto:jason.swails.gmail.com]
> ·¢ËÍʱ¼ä: 2013Äê6ÔÂ29ÈÕ 4:31
> ÊÕ¼þÈË: AMBER Mailing List
> Ö÷Ìâ: Re: [AMBER] avgcoord in AT13
>
> On Fri, Jun 28, 2013 at 3:51 PM, Hongyi WU <why0713.sjtu.edu.cn> wrote:
>
> > Hello,
> >
> >
> >
> > I have just updated AmberTools to AT13, trying to use the command
> avgcoord.
> >
> > However, I still get the following error:
> >
> >
> >
> > $ cpptraj -i test.CA.cpptrajin -p T_2HHB.prmtop -y T_2HHB_md3.mdcrd
> >
> >
> >
> > CPPTRAJ: Trajectory Analysis. V13.10
> >
> > ___ ___ ___ ___
> >
> > | \/ | \/ | \/ |
> >
> > _|_/\_|_/\_|_/\_|_
> >
> > INPUT: Reading Input from file test.CA.cpptrajin
> >
> > [avgcoord 1.CA out CA.coords]
> >
> > [avgcoord]: Command not found.
> >
> >
> >
> > I've learned from http://archive.ambermd.org/201305/0324.html that
> > avgcoord has indeed been implemented into AT13. So did I miss
> > something?
> >
>
> It's the "average" action, not 'avgcoord'. It was "average" in ptraj, too.
>
> The AmberTools manual has a full listing and description of available
> commands in cpptraj.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Jun 29 2013 - 08:00:02 PDT
