Re: [AMBER] ptraj atomicfluct

From: Thomas Cheatham <>
Date: Sat, 24 Mar 2012 15:26:16 -0600 (Mountain Daylight Time)

> 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 - 14:30:04 PDT
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