Hello,
On Wed, Mar 3, 2010 at 1:00 PM, Denny Bromley <dbromley.u.washington.edu> wrote:
> Thank you Jason, the world is becoming much more clear. :)
>
> After I have parameterized my molecules (in my case, all 20 residues,
> benzene, and a couple of other fairly normal molecules) using Antechamber,
> the atom types output in the mol2 file will be GAFF atom types along with
> their partial charges, correct? In this case, to get the vdw radii of these
This is correct. Charge information is separate from the rest of the
parameters (for good or bad). Charge information is found in either
the OFF library files whereas all other parameters are found in parm
files or force modification (frcmod) files.
> atoms, should I look in the gaff.dat file in the parms directory? When I do
> this I see this:
>
>
> MOD4 RE
> h1 1.3870 0.0157 Veenstra et al JCC,8,(1992),963
> h2 1.2870 0.0157 Veenstra et al JCC,8,(1992),963
> h3 1.1870 0.0157 Veenstra et al JCC,8,(1992),963
> h4 1.4090 0.0150 Spellmeyer, one electrowithdr.
> neighbor
> h5 1.3590 0.0150 Spellmeyer, two electrowithdr.
> neighbor
> ha 1.4590 0.0150 Spellmeyer
> hc 1.4870 0.0157 OPLS
> hn 0.6000 0.0157 !Ferguson base pair geom.
> ho 0.0000 0.0000 OPLS Jorgensen,
> JACS,110,(1988),1657
> hp 0.6000 0.0157 same to hs (be careful !)
> hs 0.6000 0.0157 W. Cornell CH3SH --> CH3OH FEP
> ....
> ....
> ....
>
>
>
> Am I parsing this correctly to read that the h1 atom type has a vdw radii of
> 1.3870 and a well depth of 0.0157?
That's how I would interpret it.
>
> Thanks again!
> -denny-
>
Good luck!
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Mar 03 2010 - 12:00:06 PST
