Re: [AMBER] Defining reaction coordinate for US

From: bharat gupta <>
Date: Thu, 7 Jul 2016 17:38:33 +0900

Hello Amber Users,

Could anybody tell me how can I define reaction coordinate for difference
in distance for a proton transfer reaction using the restraint file for
Umbrella Sampling?

Oe1-He1 (Asp) C-O4(glycosidic bond). So, for the proton transfer from Asp
to glycosidic bond's oxygen, I want to provide the reaction coordinate as
difference in distance between Oe1-He1 and He1-O4. How shall I provide the
restraint file for this?

Thanks in advance for help.

*Best Regards*
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Received on Thu Jul 07 2016 - 02:00:03 PDT
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