Thank you, Francois! I indeed have tried different non-standard
procedures, and did the MD run. Actually, the difference on the resulted
charges are quite trivial. All of them can reproduce experimental values
close, though not ideal. The problem might on the VDW parameters side.
In 1992, Gough et al derived the parameters for F atom. They first
fitted the charges by non-RESP method, and then tuned the VDW parameters
to fit the experimental density and enthalpy of vaporization. Now since
Amber force fields uniformly use RESP derived charges (correct me if I
am wrong here), I guess the the F atom need to be re-parametrized.
Thanks,
Mingfeng
On Wed, 2006-12-20 at 08:21 +0100, FyD wrote:
> Quoting Mingfeng Yang <mfyang.gmail.com>:
> Look for:
> - the table '%Tatoms' line 302 in R.E.D.-II, & add the 'F' atom in the
> corresponding list with its atomic number, i. e. something like: F =>
> "9"
> - the table '%Elements' line 1524 in R.E.D.-II, & add the 'FT' atom in
> the corresponding list with its atomic number, i. e. something like:
> FT => "9"
>
> You should get what you wish with the following type of atom name
> conventions in the initial PDB file:
> C1 F2 F2 F2 C3 H3 O4 H4 C1 F2 F2 F2 : default RESP charge derivation
> CT1 FT2 FT2 FT2 C3 H3 O4 H4 CT1 FT2 FT2 FT2: non-standard RESP charge
> derivation.
> You can obviously try many other possibilities...
> I hope this helps, regards, Francois
>
>
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Received on Sun Dec 24 2006 - 06:07:11 PST
