Dear Dan,
I recently installed AmberTools 1.5 on my Linux machine.After the
installation, i ran the rms command in ptraj and its showing the folowing
error :
PTRAJ: reference ref.pdb
PTRAJ: rms reference out prot.rms .CA
WARNING in ptraj(), rms to reference: missing reference structure.
Set this prior to this rms with the command "reference"
Ignoring command...
The reference file - ref.pdb is in the working directory!
Could you please help??
Thanks
Po
On Wed, Jun 15, 2011 at 9:28 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Yes, unfortunately I haven't yet included the 'previous' functionality
> in the cpptraj RMS action, though it will probably be there sometime
> in the not too distant future.
>
> -Dan
>
> On Tue, Jun 14, 2011 at 11:38 PM, Xiao Chen <chen.xiao.po.gmail.com>
> wrote:
> > 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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> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
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> >>
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> >
>
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Received on Tue Jun 14 2011 - 21:30:03 PDT
