AMBER Archive (2004)

Subject: AMBER: restraintmask problem in ptraj

From: Takanori TANAKA (gouhan_at_biochem.s.u-tokyo.ac.jp)
Date: Mon Nov 15 2004 - 05:06:23 CST

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
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