AMBER Archive (2006)

Subject: AMBER: about Silica's polarizability

From: yxiong99 (
Date: Thu Aug 03 2006 - 10:20:19 CDT

Dear sir,
   In AMBER force field, I know the following parameters mean that atom type, Atomic mass and the atomic polarizability respectively. However, why have some atoms not polarizability such as CU,Fe,Rb,Cs,Zn?
   I am setting up NEW parameter for Silica. I have found a paper in which many parameters for silica are calculated for CHARMM force field. (J. Phys. Chem. B 2006, 110, 2782-2792). But I don't find polarizability for Silica. So what should be for Silica's polarizability ?
Which module will the polarizability parameter be used in? I am doing MMGBSA calculation. Whether is polarizability important for MMGBSA?
P 30.97 1.538 phosphate,pol:JACS,112,8543,90,K.J.Miller
S 32.06 2.900 S in disulfide linkage,pol:JPC,102,2399,98
SH 32.06 2.900 S in cystine
CU 63.55 copper
FE 55.00 iron
Li 6.94 0.029 lithium, ions pol:J.PhysC,11,1541,(1978)
IP 22.99 0.250 assumed to be Na+ (ion plus)
Na 22.99 0.250 Na+, ions pol:J.PhysC,11,1541,(1978)
K 39.10 1.060 potassium
Rb 85.47 rubidium
Cs 132.91 cesium
Zn 65.4 Zn2+
LP 3.00 0.000 lone pair
Any information will be appreciated!
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