[AMBER-Developers] start of files for a new "ff09" force field

From: case <case.biomaps.rutgers.edu>
Date: Fri, 3 Jul 2009 15:36:40 +0100

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.


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Received on Mon Jul 06 2009 - 17:17:48 PDT
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