Re: [AMBER] parameterizing a connected moiety

From: FyD <>
Date: Fri, 18 Jul 2014 15:38:11 +0200

Dear Mohammad,

> 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?

You could use R.E.D. Server Dev./PyRED at to generate a
force field for molecular fragment(s):


regards, Francois

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Received on Fri Jul 18 2014 - 07:00:03 PDT
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