Re: [AMBER] how to allign the protein with average pdb

From: Jason Swails <>
Date: Mon, 28 Jun 2010 07:35:50 -0400

You need to load the average in as a reference, then use the "rms" command.
However, you need to use the "rms" command before you generate the average
structure, also.

trajin trajectory.mdcrd

rms first mass

average avg.pdb pdb

Then use that pdb as a reference:

trajin trajectory.mdcrd
reference avg.pdb

rms reference mass
atomicfluct _________ (I forget the exact usage).

Good luck!

On Mon, Jun 28, 2010 at 2:50 AM, REENU KHATTRI <>wrote:

> hello sir i am calculating rmsd residue wise but result is not good i want
> to first align or superimpose the protein with average pdb and use this
> trajout file to perresidue wise calculation is any command to align a
> protein.
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Mon Jun 28 2010 - 05:00:04 PDT
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