Thank you Dan.
One last question. Is it possible to use a PDB file as reference? If yes, what is the syntax. Haven’t found it in the manual and
“reference my.pdb” doesn’t work.
Regards
George
> On 21Feb, 2015, at 6:39 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi,
>
> On Sat, Feb 21, 2015 at 2:14 PM, George Tzotzos <gtzotzos.me.com <mailto:gtzotzos.me.com>> wrote:
>
>> parm 4fqt_solv.prmtop
>> trajin prod_0-100ns.nc
>> reference 4fqt_solv.inpcrd
>> reference prod_0-100ns.nc [last]
>>
>
> If you want to select the last frame you have to use 'lastframe' - last is
> only for 'trajin' / 'ensemble'.
>
>
>>> rms ToLast :10-125&!.H= ref [last] rmsd.agr
>> RMSD: (:10-125&!.H*), reference is reference frame prod_0-100ns.nc
>> (:10-125&!.H*), with fitting.
>> Warning: [rms] Not all arguments handled: [ rmsd.agr ]
>>
>
> Here you are missing an 'out' keyword. You want:
>
> rms ToLast :10-125&!.H= ref [last] out rmsd.agr
>
> Hope this helps,
>
> -Dan
>
>
>> run
>> xmgrace rmsd.agr
>> DATASETS:
>> 2 data sets:
>> Xray "Xray" (double), size is 10000
>> ToLast "ToLast" (double), size is 10000
>> DATAFILE OUTPUT:
>> rmsd.agr: Xray
>> rmsd.agr: Writing 10000 frames.
>> No output is produced for the 2nd dataset [ToLast]
>>
>> My question is what is the missing argument in defining the 2nd reference
>> structure?
>>
>> Thanks in advance for your suggestions
>>
>> George
>>
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>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/ <http://home.chpc.utah.edu/~cheatham/>
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Received on Sat Feb 21 2015 - 14:00:03 PST
