Re: AMBER: Disulfide Problem

From: David A. Case <>
Date: Thu, 1 Mar 2007 09:00:31 -0800

On Thu, Mar 01, 2007, Beale, John wrote:

> Taking out the CONNECT and SSBOND lines in the pdb file seems to have
> corrected the problem with LEaP crashing when I use the "bond" routine
> on the SG atoms. I did change the CYS to CYX. Now, when I use the
> "bond" routine the structure in the edit window shows up with the
> correct disulfide bonds. The pdb file saved out of leap shows that the
> disulfide bonds have become disconnected. This is also true of pdb files
> generated with ambpdb using *.rst files from minimizations or dynamics
> runs.

LEaP does not put CONECT records into pdb files when writing them. So, you
cannot tell from that whether the bond is there or not. Please use the "desc"
command in LEaP to see what bonds are present (or use the visualization tool
in xleap.)

So, you can either leave in the original CONECT records and not use the "bond"
command, or leave them out and use it. Since there are no CONECT records in
the output pdb files, looking at things in Chimera may not be of much help.

(I'm cc-ing this to Wei Zhang: we need to make sure that sleap gives a useful
message if a user tries to add a bond that is already present in the


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Mar 04 2007 - 06:07:41 PST
Custom Search