From: Jason Swails <>
Date: Thu, 18 Sep 2014 11:58:02 -0400

On Thu, 2014-09-18 at 21:17 +0530, Sourav Purohit wrote:
> Okay. So is there no other way around this problem??? Kindly share ur
> thoughts on this.

First of all, be sure that this is actually a problem -- it could be
that the minimizer is able to right itself eventually. It also could be
that it happens on few enough frames that you can safely omit the ones
that won't minimize. It could be that there is something seriously
wrong with your structure (dangling termini, missing disulfide bonds,
etc.). This will require some investigation on your part (visualization
is your friend here).

If it _is_ still a problem, then you will have to find another program
that implements a better minimizer than Amber. Within Amber, there is
no other option to minimize your structure that I am familiar with (but
I have typically had good luck with XMIN).

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Sep 18 2014 - 09:30:05 PDT
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