AMBER Archive (2008)

Subject: AMBER: 2D RMS plot

From: Steve Spronk (spronk_at_umich.edu)
Date: Wed Jun 11 2008 - 14:18:32 CDT

I would like to create a 2D RMS plot for my MD trajectory, but I'm having
trouble figuring out how to do so. According to the rdparm documentation, I
should use this program to create one. But I keep getting a strange error.
This occurs whether I use the latest version of AmberTools or our older
version of amber (amber 8).

 

Here are my commands:

$ rdparm 1w50.nowat.prmtop

RDPARM MENU: rms 1w50.nowat.1-11-50.mdcrd

 

WARNING in dispatchToken: Token string "rms" not found in tokenlist

 

 

WARNING in dispatchToken: Token string "1w50.nowat.1-11-50.mdcrd" not found
in tokenlist

 

 

RDPARM MENU: rms

 

WARNING in dispatchToken: Token string "rms" not found in tokenlist

 

 

RDPARM MENU: quit

EXITING program...

 

For what it's worth, other commands seem to run fine, and I have used the
prmtop file numerous times. I looked in the source code for rdparm, and
indeed, rms is not among the tokens in rdparmTokenlist, although the help
still discusses it and even has a "help rms" entry for it. Any help would
be greatly appreciated!

 

Thanks,

Steve

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