Re: [AMBER] parameterizing a connected moiety

From: Jason Swails <>
Date: Thu, 17 Jul 2014 14:51:14 -0700

For starters, I suggest looking at, which walks through a
very similar project. You might get some good ideas.

n Thu, Jul 17, 2014 at 2:31 PM, Mohammad Salem <>

> ​​
> 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 b
> ​​
> ackbone. 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
> ​​
> .

​I would urge against hydrogen caps. Quoting from the tutorial I gave you:

... we need to deal with the bond that would normally link the dye to the
linker. This needs to be capped before beginning the geometry optimization.
In theory one could use any form of cap, however, it is important to
remember that the cap will not be present in the actual simulation and yet
the charges on the non-cap atoms must sum to the correct integer charge.

So in your charge derivation, you would have to constrain your capping
hydrogen atoms to have a net ​charge of 0, which will in all likelihood
result in poor fits to the electrostatic potential in that region of the
molecule. I would suggest using a different type of cap (maybe a methyl
group, for instance), and make sure to constrain the net charge of the cap
to be 0. R.E.D. automates this procedure.

> 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?

​Bond and angle parameters are fairly transferrable, so you can find
analogous parameters in the parameter files and copy those to your frcmod
file. Dihedral parameters are less transferrable. You should find one
that looks close to what you have and then run some quick test simulations
to make sure it is behaving reasonably. You may have to fit the torsion
parameters to a QM scan to improve behavior.

The tutorial I sent you suggested the approach of just running tleap and
taking note of the parameters it couldn't find. (You'll need to do this in
2 steps -- once for the bonds and angles and a second time for the


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Jul 17 2014 - 15:00:03 PDT
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