AMBER Archive (2008)

Subject: Re: AMBER: "Dumping RAW 2D RMS data is not yet implemented"?

From: Jianyin Shao (jyshao2004_at_gmail.com)
Date: Tue Jun 17 2008 - 10:36:01 CDT

Hi, Steve,

Please download the newest ptraj-9.9h from Dr. Cheatham's website. (
http://www.chpc.utah.edu/~cheatham/software.html)

Best,

Jianyin

On 6/17/08, Steve Spronk <spronk_at_umich.edu> wrote:
>
> Hi all,
>
>
>
> I'm trying to create a 2D RMS plot for my system. I am using the new
> AmberTools suite of analysis programs from amber10. Here is the ptraj input
> file (ptraj_2drms_raw.in):
>
>
>
> trajin ../../1sgz.nowat.1-11-10.mdcrd
>
> 2drms out 2drms_raw.txt raw :73-80_at_N,CA,C
>
>
>
> But when I run it with this command,
>
>
>
> $ ptraj ../../1sgz.nowat.prmtop ptraj_2drms_raw.in
>
>
>
> everything works fine until the end. The last two lines are as follows:
>
>
>
> Dumping 2D RMS data to file 2drms_raw.txt
>
> Dumping RAW 2D RMS data is not yet implemented...
>
>
>
> The output file 2drms_raw.txt is empty. I looked at the source code in
> actions.c, and the raw data dumping definitely **is** implemented in
> there. So it's strange that it doesn't work. Even stranger, I can't find
> the source of this output. When I grep for "RAW 2D RMS" in any of the ptraj
> programs, nothing is found. When I grep "not implemented" in the ptraj
> programs, there are four lines found but none of them are related at all to
> the 2D rms data.
>
>
>
> I've worked around it by just writing out the file as plotmtv and parsing
> that output to pull out the raw data. But I'm very curious about what's
> happening with the raw command. Any help is appreciated.
>
>
>
> Thanks,
>
> Steve
>

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