molecular weight ?? ?? -- Is it not used when calculating energy? c 12.01 0.616 Sp2 C carbonyl group c1 12.01 0.360 Sp C c2 12.01 0.360 Sp2 C c3 12.01 0.878 Sp3 C Ebond = kr*(r-r0)^2 bond kr r0 ow-hw 553.0 0.9572 TIP3P water br-br 123.2 2.542 SOURCE1 4 0.0000 0.0000 br-c 240.3 1.946 SOURCE2 2 0.0285 0.0285 Eangle = kth*[(th-th0)*pi/180.0]^2 angle kth th0 hw-ow-hw 100. 104.52 TIP3P water hw-hw-ow 0. 127.74 (found in crystallographic water with 3 bonds) br-c -br 66.9 113.10 SOURCE0 1 br-c -c3 63.3 110.74 SOURCE3 1 0.0000 0.0000 I'm much confusing with this part. How to use these parameter to calcuate Etorsion? Why the second column does not exist in certain torsion such as "c2-c3-c2-hc"? What is the function of second column when calcuate Etorsion. What is the meaning of positive and negative n? Etorsion = 0.5 * Vn * [ 1 + cos( n * phi - gamma ) ] ---- ( I guess ) torsion ?? Vn gamma n X -c -c -X 4 1.200 180.000 2.000 X -c -c1-X 2 0.000 180.000 2.000 X -c -cg-X 2 0.000 180.000 2.000 same as X-c-c1-X c3-c3-os-c 1 0.383 0.0 -3. Junmei et al, 1999 c3-c3-os-c 1 0.80 180.0 1. Junmei et al, 1999 c3-os-c3-os 1 0.10 0.0 -3. Junmei et al, 1999 c2-c3-c2-hc 1.1 180. 2. Junmei et al.1999 c2-c3-ca-hc 1.1 180. 2. Junmei et al.1999 c2-hc-c -o 1.1 180. 2. Junmei et al.1999 d = distance(i,j); a = d/(ri + rj); Eab = sqrt(Ea*Eb); Evdw = Eab*(1.0 / a^12 - 2.0 / a^6) vdw r E 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