AMBER Archive (2008)

Subject: RE: AMBER: 2D RMS plot

From: Steve Spronk (spronk_at_umich.edu)
Date: Thu Jun 12 2008 - 07:42:41 CDT

Thank you! The information on the 2drms command in ptraj is not in the
User's Guide that came automatically with the AmberTools download. Thank
you for pointing me to the correct information.

Steve

 

  _____

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Jianyin Shao
Sent: Wednesday, June 11, 2008 6:18 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: 2D RMS plot

 

Hi, Steve,

2D rms command does not work in rdparm. It should be used in ptraj. Please
see the following link for the usage of 2drms command.
(http://www.chpc.utah.edu/~cheatham/ptraj.html)

Best,

Jianyin

On 6/11/08, Steve Spronk <spronk_at_umich.edu> wrote:

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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