Thanks Dan!
I was wondering about the keyword "previous" from the rms command in ptraj,
is not available anymore for cpptraj? I have gone through the manual for the
cpptraj command and this option is not available.
Po
On Mon, Jun 13, 2011 at 8:25 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> 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.
>
> -Dan
>
>
> On Mon, Jun 13, 2011 at 6:39 AM, Xiao Chen <chen.xiao.po.gmail.com> 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 Tue Jun 14 2011 - 21:00:03 PDT
