AMBER Archive (2007)

Subject: Re: AMBER: Backbone atoms

From: David A. Case (case_at_scripps.edu)
Date: Sat Dec 08 2007 - 16:58:30 CST

On Sat, Dec 08, 2007, Boutheina Kerkeni wrote:
>
> I have a question concerning the backbone atoms of an entire protein
> from a pdb file: I need to specify these in order
> to compute RMSd using ptraj. (@...?) I have 796 Residues.

You can use the ambmask program to experiment and figure out things like this
on your own. Further, one of the examples in the "ambmask" section of the
Users' Manual seems to be exactly what you are asking for.

...dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu