AMBER Archive (2008)

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

From: Yong Duan (
Date: Mon Jan 14 2008 - 22:14:26 CST

You need to give us more detail.
You are using sybyl, or AMBER? How did you make the AMBER topology file?
Sybyl, as far as I know, does not understand AMBER topology file.
Just to make it very clear. I do not doubt that physically there should be a
bond. The question is whether you put it in the topology file. If you made
in sybyl, it may not be translated to AMBER.
Bottom line, check the amber topology file.
No, it is not because your computer.
-----Original Message-----
From: [] On Behalf Of
捞毛 渔
Sent: Monday, January 14, 2008 4:12 PM
Subject: 回复: RE: AMBER: Disturb you for help !?=

Dear Dr Yong Duan,
Thanks for your quik reply! When I observed the molecular in the sybyl, I
found the bonds were disconnected. Then I connected them in the sybyl,
However, during the minimization process the same problem still appeared. Is
this a reason of my computer?
Can you provide me a help?

Best wishes
Rilei Yu



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