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Daniel tells me that "avgcoord" has been replaced by "vector center"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]
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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Received on Fri Jun 28 2013 - 19:00:02 PDT
