Thank you very much for the help.
I have an additional question. The backbone rmsd of the protein I'm working on is within 1.2 angstrom of the crystallographic structure. Yet the atomic fluctuations on the same trajectory range between 4-9 angstrom.
How can this be explained?
On Mar 24, 2012, at 10:26 PM, Thomas Cheatham wrote:
>
>> This works. However when I try to fit to the average structure
>>
>> trajin mdcrd
>> rms average.pdb
>> atomicfluct out back.apf .C, CA, N byatom
>>
>> ptraj complains of syntax error.
>
> Why do you think that "rms average.pdb" would work? If you read the ptraj
> or cpptraj manuals, you can see the appropriate syntax. For ptraj, you
> need to specify a reference structure and then rms reference
>
> reference average.pdb
> rms reference mass
>
>
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Received on Sat Mar 24 2012 - 15:00:02 PDT
