[gmx-users] Free energy perturbation of Cu(I) binding

abhigna polavarapu abhignap at gmail.com
Fri Feb 6 01:26:42 CET 2009

Hey Mark,
 I am just not getting the theory behind doing position restraints and
applying them to equilibrate. So let me frame my question well. Cu(I)
is binding to three amino acids in the protein. Now If I remove Cu(I)
the -1 charge of the protein changes to 0. So the protein has two
specific charge states which it should equilibrate. So coming to
position restraint should I restrain the total protein when I remove
Cu from the structure or just the copper binding core and how does
restraining help the protein from destabilizing due to huge
electrostatic interactions. I looked for this in the manual but could
not understand it properly and was not sure what I am doing.
Please help me out here.
Thank you

On Tue, Feb 3, 2009 at 10:36 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> abhigna polavarapu wrote:
>> Thanks Mark, thats what I really wanted to do. So can you please let
>> me know where I can find out the way to do position restraints and to
>> know how these work.
> Chapter 5 in the manual, or some tutorial material (perhaps from the wiki).
> Mark
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