AMBER Archive (2008)

Subject: AMBER: RE: 回复： AMBER: RE: 回复： RE: AMBER: Disturb you for help !?=

From: Yong Duan (duan_at_ucdavis.edu)
Date: Tue Jan 15 2008 - 01:40:39 CST

 
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Can you please describe exactly what happened? You received "core dump"
error message? Miminized by sander? Then, how did you realize the bonds are
broken? After the error message and from the partially minimized structure?
 
 
yong
 
-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
捞毛 渔
Sent: Monday, January 14, 2008 9:34 PM
To: amber_at_scripps.edu
Subject: 回复： AMBER: RE: 回复： RE: AMBER: Disturb you for help !?=

Dear Yong Duan,
The compound was the docking result using sybyl. When I displayed the
compound in the sybyl, I found two bonds were not connected. So i connected
them in sybyl. Then I use amber to generate the topology file. Before it
was minimized I display them in xleap. And the bonds were all connected. But
when compound was minimized before md, there was an error said that the core
was out. Then it program failed. I attached the file to this email.
 
Best wishes
 
Rilei Yu

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