[AMBER] parameterizing a connected moiety

From: Mohammad Salem <mohammad.alaraby.gmail.com>
Date: Thu, 17 Jul 2014 15:31:15 -0600

Dear Amber users,

I am new to Amber, so I appreciate your patience.

I am working on a fluorescent protein and the chromophore of it is part of the backbone. I want to edit this chromophore and I need re-parameterize it. I extracted that moiety and capped the trimmed connections with Hydrogens and did it with antechamber. Now the problem is that their are connections (bonds) between the chromophore and the protein and there are no parameters for these.

Is it safe to borrow the parameters of regular amino acids and edit the parameter file to include parameters between atoms of the chromophore and the rest of the protein? If so, do I have to do it manually, or there is a better trick?

Thanks a lot for your time!

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Received on Thu Jul 17 2014 - 15:00:02 PDT
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