Re: [AMBER] cpptraj RMSD stats

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Tue, 18 Aug 2015 09:34:46 -0600

What version of cpptraj are you running? Make sure you're using an
up-to-date version of cpptraj.

-Dan

On Tue, Aug 18, 2015 at 9:18 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Thank you Dan,
>
> I run the script as you suggested. It produced the error shown at the end of the message.
>
> Does avg refer to an average structure that I should had produced before running rms?
>
> [3n7h_new.pdb] is a PDB file, Parm 3n7h_new.pdb (reading 1 of 1)
> [rms R0 reference out rmsd.agr .CA]
> RMSD: (.CA), reference is reference frame 3n7h_new.pdb (@CA), with fitting.
> [avg R0 out Avg.rms.dat]
> [avg]: Command not found.
>
>
>> On 18 Aug 2015, at 16:50, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>
>> I think you can get what you want with the 'avg' analysis command. For example:
>>
>> parm 3n7h_de3_solv.prmtop
>> parm 3n7h_new.pdb
>> reference 3n7h_new.pdb parm 3n7h_new.pdb
>> rms R0 reference out rmsd.agr .CA
>> avg R0 out Avg.rms.dat
>>
>> Hope this helps,
>>
>> -Dan
>>
>> On Tue, Aug 18, 2015 at 7:43 AM, George Tzotzos <gtzotzos.me.com> wrote:
>>> In running cpptraj rmsd is there a way to generate stats of the type
>>>
>>> id mol avg sd min max num
>>> 0 3n7h_de3_solv.prmtop 1.296 0.214 0.792 2.058 2000
>>> 1 3n7h_new.pdb 0.000 0.000 0.000 0.000 0
>>>
>>> Thanks in advance for any suggestions
>>>
>>> Regards
>>>
>>> George
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> 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/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
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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/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Aug 18 2015 - 09:00:04 PDT
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