AMBER Archive (2007)

Subject: Re: AMBER: Polarizable potential

From: David A. Case (case_at_scripps.edu)
Date: Wed Nov 28 2007 - 10:19:06 CST

On Wed, Nov 28, 2007, Denis Courtier wrote:

> I am trying to mimic a N-Ac proline molecule into a polarizable potential.
>
> When i run leaprc.ff02polEP.r1into xleap, Am I charging polarizable
> parameters for any molecule? In this case, which are these molecules?

You are loading parameters for *standard* amino acids and nucleotides.

For non-standard residues, you have to create the parameters yourself. For
your example, however, setting the system up as ACE-PRO might do the trick.

[I don't recommend using ff02polEP.r1; only the non-EP version, ff02pol.r1
was really checked for its protein behavior. And, all of these backbone
modifications are probably irrelevant anyway for a single proline residue.]

...dac

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