Hi,
On Mon, 25 Feb 2008, Scott Brozell wrote:
> Have there been any developments for silicon parameters ?
> The context is docking studies of ligands with silicon as a
> cogener of carbon.
This was created by using the corresponding c3 gaff values
except for the nonbonded terms which are from DOCK.
Comments are welcome.
DOCK Amber Score Tetrahedrally Bonded Silicon
MASS
Si 28.085
BOND
ca-Si 323.5 1.513 gaff c3-ca
c3-Si 303.1 1.535 gaff c3-c3
oh-Si 314.1 1.426 gaff c3-oh
ANGLE
ca-ca-Si 63.6 112.47 gaff Si -> c3
ca-Si-c3 62.5 114.61 gaff Si -> c3
ca-Si-oh 67.2 112.97 gaff Si -> c3
c3-c3-Si 63.2 110.63 gaff Si -> c3
c3-Si-c3 63.2 110.63 gaff Si -> c3
c3-Si-oh 67.7 109.43 gaff Si -> c3
Si-c3-hc 46.4 110.05 gaff Si -> c3
Si-oh-ho 47.1 108.16 gaff Si -> c3
DIHE
ca-ca-Si-c3 6 0.000 0.000 2.000 gaff X -c3-ca-X
ca-ca-Si-oh 6 0.000 0.000 2.000 gaff X -c3-ca-X
ca-Si-c3-c3 9 1.400 0.000 3.000 gaff X -c3-c3-X
ca-Si-c3-hc 9 1.400 0.000 3.000 gaff X -c3-c3-X
ca-Si-oh-ho 3 0.500 0.000 3.000 gaff X -c3-oh-X
c3-c3-Si-c3 1 0.18 0.0 -3. gaff c3-c3-c3-c3
c4-c3-Si-c3 1 0.25 180.0 -2. gaff c3-c3-c3-c3
c3-c3-Si-c3 1 0.20 180.0 1. gaff c3-c3-c3-c3
c3-c3-Si-oh 9 1.400 0.000 3.000 gaff X -c3-c3-X
c3-Si-c3-hc 1 0.16 0.0 3. gaff Si -> c3
c3-Si-oh-ho 1 0.16 0.0 -3. gaff ho-oh-c3-c3
c3-Si-oh-ho 1 0.25 0.0 1. gaff ho-oh-c3-c3
c3-Si-oh-ho 1 0.25 0.0 1. gaff Si -> c3
oh-Si-c3-hc 1 0.25 0.0 1. gaff Si -> c3
IMPROPER
Si-ca-ca-ca 1.1 180.0 2.0 Using default value
NONBON
Si 2.220 0.320 DOCK vdw_AMBER_parm99.defn
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Received on Sun Mar 02 2008 - 06:07:35 PST
