Dear Julio (and others who maybe interested),
I have uploaded QM data on methyl phosphate and ethyl phosphate, both with a -2 formal charge, to the Wolf2Pack database. There is target QM data for all unique bond (i.e. 9 total), angle (i.e. 11 total) and torsion (i.e. 4 total) angles present in these molecule - for more than 1000 QM data points. This included relative energies computed at HF/6-31G(d)//HF/6-31G(d), B3LYP/6-311++G(2d,2p) (i.e. that used to parameterize Glycam06), and MP2/cc-pVDZ//HF/6-31G(d). Partial atomic charge sets for these molecules have also been computed (using R.E.D.) such that they are compatible for parameter optimization for Glycam06, Parm99SB, and Gaff. You will notice that the bond and angle curves are quite different between the three theories, especially with the placement of the minimum value. You may want to consider reproducing HF/6-31G(d) or MP2/cc-pVDZ curves, even though the B3LYP data would be consistent with Glycam06 parameterization. The goal is to have MM reproduce a curve that is considered reliable and results
in reproduction of experimental observation - this was our overriding philosophy in developing Glycam06.
Methyl phosphate with a -1 formal charge is also present in the database with > 1100 QM target data points. There are three conformations represented for the molecule. I will upload sometime soon ethyl phosphate (-1) to W2P's database.
Best Regards,
Karl
----- Original Message -----
From: "Julio Dominguez" <acheron24.hotmail.com>
To: amber.ambermd.org
Sent: Friday, August 23, 2013 4:43:17 AM
Subject: Re: [AMBER] AMBER Digest, Vol 587, Issue 1
Frank,
Sorry for the late reply; I think that we are going for the -2 version of phosphate.
Thank you very much.
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Received on Fri Aug 23 2013 - 07:00:02 PDT
