Re: [AMBER] keyword ref

From: Daniel Roe <>
Date: Mon, 13 Jun 2011 10:55:33 -0400


I presume you are referring to the keywords for the 'rmsd' action. You
can specify an external reference structure for an rms command in
three different ways:

refindex <#>: Use reference structure read in by a previous "reference
<filename>" command, where <#> is the order the reference was read in.
ref <filename>: Use reference structure read in by a previous
"reference <filename>" command.
reference: Short for "refindex 0" (first reference structure read in),
included for backwards compatibility with ptraj.

For example, given the script:

trajin mdcrd
reference ref1.rst7
reference ref2.rst7
rmsd reference :1-10 out r1.dat
rmsd refindex 1 :1-10 out r2.dat
rmsd ref ref2.rst7 :1-10 out r2.dat

The first rms command will use ref1.rst7 as a reference, and the last
two rms commands will use ref2.rst7 as an index. See the manual for
more details. Let me know if you still have questions.


On Mon, Jun 13, 2011 at 6:39 AM, Xiao Chen <> wrote:
> Hi All,
> Can you clearly elucidate the difference between the keywords "ref" and
> "reference" in cpptraj.
> Thanks!
> Po
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Received on Mon Jun 13 2011 - 08:00:04 PDT
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