Hello Xiaoquan,
The equation used for modeling improper dihedral energetics is the same as that used for normal traditions. The equation that you have written is correct. I also would consider your force constant to be large in comparison to the magnitude of other improper terms. However, other normal dihedral terms are likely to contribute to this out-of-plane motion (e.g. ca-ca-ca-ca, ha-ca-ca-ca, ca-ca-ca-sy, and ha-ca-ca-sy). Depending on these terms, your large force constant maybe trying to compensate for them. I typically parameteize the normal dihedral angles first, and then "soak up" any remaining error in the potential energy surface using the improper dihedral term.
With that said, if your force constant correctly reproduces the potential energy surface and you will not be using it in other systems (i.e. you don't want it to be transferable between molecules) with a different local chemical environment (e.g. a molecule containing a c3-ca-ca-sy term), then you are probably okay in using it to model benzenesulfonic acid.
Best regards,
Karl
----- Original Message -----
From: "X Sun" <egeh00.aol.com>
To: "askamber" <amber.ambermd.org>
Sent: Tuesday, August 20, 2013 9:47:29 PM
Subject: [AMBER] Huge improper dihedral fitting coefficient.
Dear all,
I have finished an improper dihedral scan, ca-ca-ca-sy. It's an improper dihedral in benzenesulfonic acid. I am not sure the equation of improper dihedral in AMBER, is that Vn(1+cos(nx-r))? I used the equation to get a vergy huge Vn, which is 58.596 kcal/(mol*rad^2), n=2.0 and r=179.01 degree. But I saw the largest Vn is 14 kcal/(mol*rad^2) in GAFF. Did I use the wrong equation?
Cheers,
Xiaoquan Sun.
2013-08-20
X Sun
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Received on Wed Aug 21 2013 - 01:00:03 PDT
