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.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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Received on Sun Jun 15 2008 - 06:07:22 PDT
