AMBER Archive (2009)

Subject: RE: [AMBER] rmsd_ptraj

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Thu Jul 09 2009 - 02:08:53 CDT

> but how to mention for all atoms ,
> they have given in archives like
> rms first out complex_equi3.crd.rmsd @CA,C,N
>
> what have to be given after @ ,

The tutorials are excellent references and worth the time to explore. For
the "mask" in the rms command either you could not list one (which
defaults to all atoms) or use * (which matches all atoms). If in doubt,
load up the prmtop in rdparm and use the "checkmask" command to see what
is selected. Also, as you run ptraj, it will print a full summary of what
it thinks it selected... As usual on this list, the best thing is to
experiment and try things out to see what you will see.

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