[AMBER] Advanced restraints in protein mutation

From: Simon Kit Sang Chu <simoncks1994.gmail.com>
Date: Wed, 6 Jun 2018 17:21:10 +0800

Hi everyone,

I am considering a mutation by appending 4 prolines at the end of
C-terminal through FEP. Therefore, there will be disappearing hydrogen atom
in the original C-terminal and appearing tetra-proline and ions.

To avoid the prolines appearing in the middle of protein when lambda
increases, I want to restrain the tetrapeptide close to and orient to the
C-terminal end before the transformation. The restraint should gradually
diminish as lambda goes to zero. It would be a catastrophe if the amino
acids appeared in inappropriate locations.

To place such restraint, the most likely way is a combination of one
distance restraint between COOH and first proline residue, one angle
restraint to locate the proline center of mass to the correct end of COOH,
and one more angle restraint to point the proline open end to COOH. These
aim to facilitate shorter FEP by placing the proline in a good location and

Is there any simpler way to restrain the tetrapeptide? Maybe combine the
first two since I am actually restraining the center of mass of the first
proline to a relative coordinate. I suspect that I would also have to
restrain the ions away from the protein?

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Received on Wed Jun 06 2018 - 02:30:02 PDT
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