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

From: Saman Yousuf ali <>
Date: Tue, 9 Aug 2016 15:08:10 +0000 (UTC)

Dear David,
I donot forgot to restrain these residues. Actually during minimization and equilibration step, I hold protein-ligand and counter ion and then gradually release restraint on both. While during unrestraint minimization and equilibration steps, all medium and protein-ligand atoms were free to move. Then I ran 5ns production with harmonic restraint on previously mentioned residues. I just want to ask you that Is it fine? My restraint protocol during MD?
 Thank you.
Best Regards, Saman Yousuf AliJunior Research Fellow,

    On Tuesday, August 9, 2016 5:02 AM, David A Case <> wrote:

 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 - 08:30:03 PDT
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