Dear Yun,
> I saw "The initial partial charges for the solute were computed from the
> crystal geometry" from the paper you referred. So I guess in order to obtain
> initial charges, I should start with either a crystal structure, if
> possible, or a QM optimized structure (at the HF 6-31G ** level?). Then use
> the HF 6-31G* and CHELPG, with a constraint of 0.01, to derive initial
> charges, which can be done automatically on R.E.D. server. And then do MD as
> specified in glycam06 paper, and then derive ensemble-averaged RESP charges
> ... This really seems to a daunting task even with only one small molecule.
>
> So if what is calculated from the newly-built force field is quite different
> from experiment, we generally still keep the charges and only modify the
> angle and dihedral parameters with some kind of chemical intuition?
In the GLYCAM approach, the conformations involved in charge
derivation are determined based on MD simulations. This is an
efficient/innovative way to weight the 'representative' conformations
to be involved in charge derivation (however, one obviously needs a
fist set of charge values to run this snapshot generation). In this
approach, the charge values cannot be reproducible and running MD
simulations to generate snapshots to be involved in charge derivation
remains quite complex/time consuming.
In the Amber approach, only representative minima (lowest QM energy
minimum/minima) are directly involved in charge derivation. Here, the
conformational search/minimum selection and QM jobs can be painful and
time consuming as well. R.E.D. allows the generation of fully
reproducible charge values independently of the QM program or input
structure used; R.E.D. Server freely provides the hardware/software
for charge derivation and force field library building; this can be
quite useful in particular when QM jobs are heavy. R.E.DD.B. and its
reviewing process allows users to generate well defined RESP and ESP
charge values, and their diffusion in the community.
Both approaches have their advantages and their limitations.
regards, Francois
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Received on Tue Sep 20 2011 - 01:30:02 PDT
