#Part of this forfield is made in UCSD in August 2008, part is taken from the amberlist help "DOCK Amber Score Tetrahedrally Bonded Silicon" and the rest is copied from gaff.dat -SiO2 forcefield MASS Si 28.08 BOND O-Si 314.1 1.426 gaff c3-oh oh-Si 314.1 1.426 gaff c3-oh ca-Si 323.5 1.513 gaff c3-ca c3-Si 303.1 1.535 gaff c3-c3 c3-ho 337.3 1.092 gaff c3-hc n3-ho 394.1 1.018 gaff hn-n3 ANGLE Si-O-Si 65.0 143.70 gaff Si -> c3 # Vashishta et al -i made up the force constant Si-oh-Si 65.0 143.70 same as above O-Si-O 70.0 109.55 gaff Si -> c3 # Vashishta et al -larger than C-Si-C force oh-Si-oh 70.0 109.55 same as above 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-c3-c3 63.2 110.63 c3-c3-n3 66.2 110.38 c3-Si-oh 67.7 109.43 gaff Si -> c3 Si-c3-hc 46.4 110.05 gaff Si -> c3 ho-c3-Si 46.4 110.05 same as above Si-oh-c3 62.1 113.41 gaff c3-os-c3 Si-oh-ho 47.1 108.16 gaff Si -> c3 ho-n3-ho 39.7 117.85 gaff hn-n-hn ho-c3-ho 39.2 109.55 gaff h1-c3-h1 n3-c3-ho 49.4 109.92 gaff h1-c3-n3 c3-c3-ho 46.4 110.07 gaff c3-c3-ho c3-n3-ho 47.1 109.92 gaff c3-n3-hn oh-c3-ho 51.1 109.50 gaff hc-c3-oh DIHE O-Si-O-Si 1 0.0 0.0 1. #gaff Si -> c3 -I set PK to zero, so torsional force is zero oh-Si-oh-Si 1 0.0 0.0 1. same as above Si-O-Si-O 1 0.0 0.0 1. #-PK set to zero, see above Si-oh-Si-oh 1 0.0 0.0 1. same as above 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 ho-c3-Si-oh 1 0.25 0.0 1. gaff h1-c3-c3-oh c3-Si-oh-c3 1 0.1 180.0 2. gaff c3-c3-os-c3 c3-Si-oh-Si 1 0.1 180.0 2. same as above c3-Si-oh-c3 1 0.1 180.0 2. same as above oh-Si-oh-c3 1 1.4 180.0 1. gaff o-c-os-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