AMBER: LJ parameters for alkynes

From: David Mobley <>
Date: Mon, 26 Nov 2007 10:07:37 -0800

Dear all,

I've been computing hydration free energies for a large set of small
molecules using the GAFF parameters and AM1-BCC charges. It turns out
that alkynes have large, systematic errors. Given that alkynes are
quite nonpolar, I doubt that charges are the problem since the
electrostatic component of the hydration free energy is so small. So,
I'm looking at LJ parameters as suspect, and in particular I'm
concerned about the well depth for triple bonded carbons (acetylene is
the simplest example, of course).

I've dug back into the literature and found that these particular GAFF
well-depths originate from Amber94 and Amber99, which apparently took
them "by analogy" from the rest of the Amber force field, which really
appears to translate to just copying them exactly from the Sp3 carbon
parameters for alkanes, for example.

In a bit of testing, I tried taking the appropriate OPLS LJ parameters
for acetylene and established that, if these were used, the systematic
errors would essentially disappear. So, new alkyne carbon LJ
parameters appear to be needed.

Anyway, here's my question: Is there a "standard" parameterization
procedure for obtaining LJ parameters for Amber that I should use? I
realize all of these are quite old, and probably no new LJ parameters
have been derived in a long time.

I'm basically trying to decide between the options of:
a) Simply using the OPLS LJ parameters (I know some Amber LJ
parameters are taken from OPLS) or
b) Deriving new Amber LJ parameters somehow

My end goal is to come up with something that could go back into an
update of GAFF, so I want to make sure that the developers are happy
with what I do.

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Received on Wed Nov 28 2007 - 06:07:19 PST
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