thanks Dave,
we also have some of our own updated side chain torsions, and I hope by the
end of the summer to have slightly tweaked protein backbone dihedral
parameters too. regarding HN in arg and lys, we've been using modified
intrinsic radii for them so may want to change the radii as well, although
we should redo the tests with your new params and see if the explicit
solvent vs GB differences hold up there too.
carlos
On Fri, Jul 3, 2009 at 10:36 AM, case <case.biomaps.rutgers.edu> wrote:
> Hi everyone:
>
> I have checked into CVS some skeleton files for a new "ff09" fixed-charge
> force field. See the leaprc.ff09 file for how these typically would be
> loaded
> into LEaP.
>
> Right now, this is just ff99SB + parmbsc0 + new atom names for nucleic
> acids
> to match PDB version 3. (Note there is a "parm09.dat" which folds
> frcmod.ff99SB and frcmod.parmbsc0 into parm99.dat.)
>
> This is not fixed in stone...the nucleic acid people can make
> recommenations
> about whether or not bsc0 should be the default. I've also included
> ions08.lib as default, rather than ions94.lib.
>
> I think Carlos has been in touch with the deshaw guys about some modified
> side chain torsion parameters for proteins -- if appropriate, those could
> go
> in here. Other suggested parameters could be incorporated as well.
>
> I will be changing some atom types soon, since my studies indicate that
> side
> chain N,H atom types in arg, lys and his need to be different from the
> backbone N,H parameters in order to get proper solvation energetics for the
> side chains.
>
> Of course, there may not be just one "ff09", but I think we all agreed at
> Sanibel to try to get a set of agreed-upon parameters into a form that
> could
> be used for testing. These new files are just a framework for doing that.
> These files will be changing, so don't start calling things "ff09" yet!
>
> As per usual, comments and suggestions are welcome.
>
> ...thx...dac
>
>
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Received on Mon Jul 06 2009 - 17:17:53 PDT
