AMBER Archive (2008)

Subject: Re: AMBER: bond command

From: M. L. Dodson (
Date: Thu Jul 10 2008 - 13:34:33 CDT

Boutheina Kerkeni wrote:
> Hi Amber users
> I have a question about bond command. I have to use it more than 100
> times, I wonder if there is a way to rather than typing each bond
> command into xleap,loading a whole file that contains these say 100
> bond lines in one go? If yes, how should such file be written, and what
> is the command to load it into xleap to build the model?
> Thanks for any light you could shed on this matter.
> Best Reagrds
> Boutheina

Look at the bondByDistance command. If you have 100 bonds that cannot
be mostly recovered using bondByDistance, something may be seriously
wrong with your structure.

Bud Dodson

M. L. Dodson
Business Email: activesitedynamics-at-comcast-dot-net
Personal Email:	mldodson-at-comcast-dot-net
Phone:	eight_three_two-56_three-386_one
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)