AMBER: restraintmask problem in ptraj

From: Takanori TANAKA <>
Date: Mon, 15 Nov 2004 20:06:23 +0900

Dear All,

Has the problem presented by Oliver Hucke at Apr 21, 2004,
titled "AMBER: restraintmask and ambmask" already been solved?
Now, I found the similer problems applying restraintmask to ptraj.

I am trying to use the restraintmask to observe fluctuation of
backbone atom or sidechain atom, individually. So I wrote in
script file for ptraj as below:

 atomicfluct out fluct1.txt .CA,C,N,O byres
 atomicfluct out fluct2.txt "!.CA,C,N,O" byres

The first line was accepted and worked normally,
but the second line causes no response after the message
"PTRAJ: atomicfluct out fluct2.txt "!.CA,C,N,O" byres"
and ptraj never finish.

Moreover, the script:

 strip ".H="

seems to be unrecognized, with the message
"Mask [.H=] represents 0 atoms !!!NO ATOMS DETECTED!!!"
though H atoms are surely included in both topology and coordinate files.

With ambmask the selection string ".CA" works.
"!.CA" returns the error with "Event not found."
(because '!' character has some special meaning in UNIX),
while "\!.CA" and ".H=" work normally.

What is wrong?

Thanks very much.

Takanori Tanaka
The AMBER Mail Reflector
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Received on Mon Nov 15 2004 - 11:53:00 PST
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