Please discard previous message. I found the answer in 28.2.5. Parameter/Reference Tagging of the Amber14 manual.
Regards
George
> On 21Feb, 2015, at 6:57 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
> 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/>
>> (801) 587-9652
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Received on Sat Feb 21 2015 - 16:30:03 PST
