AMBER Archive (2003)

Subject: Re: AMBER: import pdb file in xleap

From: Vikas Varshney (vikas_var_at_rediffmail.com)
Date: Thu Aug 07 2003 - 14:21:32 CDT

Hi Mikyung..
about your second question.. for removing atoms efficiently
without any
segmentation fault, first remove the bond between the atoms. Then
remove the atom
which has no bonds now. If you click on the atom which is bonded
to someone,
xleap would crash. First make sure that the atom you are going to
delete is lone.. No
bonds..
Hope this would be of your help..

Vikas
On Fri, 08 Aug 2003 Mi-Kyung Seo wrote :
>Hi Amber users,
>
>I have two questions about xleap. (Version: Amber 7.0)
>
>1. When I open pdb file which is created by Insight and edit this
>unit (unit editor),
the structure contatins only dots, no bonds.
>However, everything is ok with pdb viewer (e.g.VMD)
>xleap can't read pdb file made from Insight??
>
>2. I got segmentation fault and xleap is closed right away when I
>build new
molecule and try to remove atom in unit editor of xleap. I clicked
"remove" button
with mouse and picked atom which I wanted to remove.
>
>Thanks.
>Regards,
>Mikyung
>
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