AMBER Archive (2008)

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

From: Steve Spronk (
Date: Tue Jun 17 2008 - 09:00:08 CDT

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 (


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


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.




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