AMBER Archive (2004)

Subject: Re: AMBER: reference with ptraj

From: Thomas E. Cheatham, III (
Date: Thu May 06 2004 - 17:12:18 CDT

> > ... to get the RMSd
> > to the average structure is has to be done in two runs, the first to
> > generate the average structure
> >
> > trajin annealing.traj 175 200
> > average average.pdb pdb
> Does 'average' automatically rms fit each frame to the 1st?
> Normally one would want to fit to the 1st frame before adding
> coordinates to avoid drift and rotation artifacts. Once an
> average structure is obtained, it is worth visualizing it
> to check for artifacts of internal motions, and then energy
> minimizing it in order to get reasonable bond lengths etc.

Yes, Bill is right here. Before doing the average you definately want to
fit otherwise the average structure could be meaningless.

   trajin annealing.traj 175 200
   rms first mass out allatoms_rmstofirst.dat *
   average average.pdb pdb *

Thanks for pointing this out Bill!


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to