Re: [AMBER] How to study the dissociation pathway for two proteins with AMBER10?

From: Jason Swails <>
Date: Fri, 19 Nov 2010 10:47:42 -0500

You can define groups if you're using a distance restraint through the
nmropt functionality. I think the groups may use center of geometry rather
than COM, but for heavy atoms they're fairly similar. See the NMR
Restraints section of the amber manual for a more thorough description of
defining groups in your distance restraints.

Good luck!

On Thu, Nov 18, 2010 at 9:59 PM, Catein Catherine <>wrote:

> Dear All,
> I am trying to study the dissociation pathway and energy between two
> proteins.
> I am wondering if we can define the dissociation pathway as one of the
> atoms in the two proteins? Are are there any way to define the dissociation
> pathway by center of mass for both proteins?
> Best regards,
> Catherine
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Fri Nov 19 2010 - 08:00:07 PST
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