Re: [AMBER] query regarding restraint on specific residues.

From: David A Case <>
Date: Tue, 9 Aug 2016 08:02:10 -0400

On Tue, Aug 09, 2016, Saman Yousuf ali wrote:
> However during unrestrained minimization step and unrestrained
> equilibration step I didn’t put restrain on the residues that I wished
> to restrain. Is it fine? or shall I apply restrain on the above
> mentioned residues (as I do not wish to analyze them) in every step of
> the simulation process? suggestions?

Depends on whether the residues you forgot to restrain moved very much from
their starting positions. Also on how important such motion would be for the
analysis you wish to make.


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Received on Tue Aug 09 2016 - 05:30:05 PDT
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