Re: [AMBER] cpptraj RMSD stats

From: George Tzotzos <gtzotzos.me.com>
Date: Tue, 18 Aug 2015 18:18:22 +0300

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
>>
>>
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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 - 08:30:05 PDT
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