The AMBER95 Force Field has been manually installed in InsightII v95.0. This was accomplished by typing in the parameters listed in Cornell, et al., A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules, J. Am. Chem. Soc., Vol 117, pp 5179-5197, 1995, also listed at The Cornell et al. 1995 AMBER force field web site.
This implementation has the following caveats:
| Atom | Description |
|---|---|
| C | sp2 carbonyl all-atom carbon and aromatic carbon with hydroxyl substituient in tyrosine |
| C* | sp2 aromatic all-atom carbon in 5-membered ring with 1 substituent |
| CA | sp2 aromatic all-atom carbon in 6-membered ring with 1 substituent |
| CB | sp2 aromatic all-atom carbon in junction between 5- and 6-membered rings |
| CC | sp2 aromatic all-atom carbon in 5-membered ring with 1 substituent and next to a nitrogen |
| CK | sp2 aromatic carbon in 5-membered ring between 2 nitrogens and with 1 hydrogen |
| CM | sp2 all-atom carbon in pyrimidine at positions 5 or 6 |
| CN | sp2 aromatic junction all-atom carbon in between 5- and 6-membered rings |
| CQ | sp2 all-atom carbon in 6-membered ring of purine between two NC nitrogens and with 1 hydrogen |
| CR | sp2 aromatic all-atom carbon in 5-membered ring between 2 nitrogens and with 1 hydrogen (in HIS) |
| CT | sp3 all-atom carbon with 4 explicit substituents |
| CV | sp2 aromatic all-atom carbon in 5-membered ring bonded to 1 N and 1 H |
| CW | sp2 aromatic all-atom carbon in 5-membered ring bonded to N-H and 1 H |
| H | amide or imino hydrogen |
| H1 | H aliph. bond. to C with 1 electrwd. group |
| H2 | amino hydrogen in NH2 |
| H3 | hydrogen of lysine or arginine (positively charged) |
| HC | explicit hydrogen attached to carbon |
| HA | amino hydrogen in NH2 |
| H4 | H arom. bond. to C with 1 electrwd. group |
| H5 | H arom. bond. to C with 2 electrwd. groups |
| HP | H bonded to C next to positively charged gr |
| HO | hydrogen in hydroxyl group |
| HS | hydrogen attached to sulfur |
| HW | hydrogen in water |
| LP | lone pair |
| N | sp2 nitrogen in amide |
| N* | sp2 nitrogen in purine or pyrimidine wiht alkyl group |
| N2 | sp2 nitrogen in base NH2 group or arginine NH2 |
| N3 | sp3 nitrogen with 4 substituents |
| NA | sp2 nitrogen in 5-membered ring with hydrogen attached |
| NB | sp2 nitrogen in 5-membered ring with lone pairs |
| NC | sp2 nitrogen in 6-membered ring with lone pairs |
| O | carbonyl oxygen |
| O2 | carboxyl or phosphate non-bonded oxygen |
| OH | alcohol oxygen |
| OS | ether or ester oxygen |
| OW | water oxygen |
| F | fluorine |
| P | phosphorus in phosphate group |
| S | sulfur in disulfide linkage or methionine |
| SH | sulfur in thiol |
| C0 | calcium ion (+2) |
| IM | chlorine ion (-1) |
| I | Iodine ion (-1) |
| IP | sodium ion (+1) |
| IB | 'big ion w/ waters' for vacuum (Na+, 6H2O) |
| QC | cesium ion (+1) |
| QK | potassium ion (+1) |
| QL | lithium ion (+1) |
| QN | sodium ion (+1) |
| QR | rubidium ion (+1) |
| CS | sp3 carbon |
| h$ | atom for automatic parameter assignment |
| c$ | atom for automatic parameter assignment |
| n$ | atom for automatic parameter assignment |
| o$ | atom for automatic parameter assignment |
| s$ | atom for automatic parameter assignment |
| p$ | atom for automatic parameter assignment |
| ospc | oxygen in SPC water molecule - used for rattle routine |
| otip | oxygen in TIP3P water molecule - used for rattle routine |
| hspc | hydrogen in SPC water molecule - used for rattle routine |
| htip | hydrogen in TIP3P water molecule - used for rattle routine |
all-atom carbon = this atom only includes the carbon---hydrogens must be explicitly defined