AMBER Archive (2001)

Subject: Re: Info about LEaP

From: David Konerding (dek_at_cgl.ucsf.edu)
Date: Mon Sep 24 2001 - 10:29:16 CDT

=?iso-8859-1?q?Paolo=20Daniele?= writes:
>Hi!
>Using the LEaP program,I got a problem:there are
>some binds among the helices of my protein,but they
>should not be! So, to remove these undesired bonds, I
>used
>the option removeBond in LEaP.
>Referring to my protein ABC, after the "check"
>command, it showed that there's, for instance, a bond
>between
>.R<GLU 36>.A<C 14> and .R<LEU 37>.A<N 1>

Hi, is that not the peptide bond?

>
>I hadn't problems giving the desc command about the
>atoms
>involved in the bonds,but when I digit the command:
>removeBond ABC.36.14 ABC.37.1
>it results in a syntax error.
>Can you help me, please?
>I'm sure of a your fast and exhaustive answer.
>Yours sincerely,

The command is "deleteBond" not "removeBond".