; ######################################################################## ; # # ; # ffamber ports for GROMACS 3.3.1 - August 2007 # ; # Eric J. Sorin - CSU Long Beach, Dept. of Chem & Biochem # ; # With significant contributions from Sanghyun Park and Jory Z. Ruscio # ; # Please cite: Sorin & Pande (2005). Biophys. J. 88(4), 2472-2493. # ; # For additional information, tools, and updates # ; # please consult http://chemistry.csulb.edu/ffamber/ # ; # # ; ######################################################################## amber94_1 79.90000 ; BR bromine amber94_2 12.01000 ; C sp2 C carbonyl group amber94_3 12.01000 ; CA sp2 C pure aromatic (benzene) amber94_4 12.01000 ; CB sp2 aromatic C, 5&6 membered ring junction amber94_5 12.01000 ; CC sp2 aromatic C, 5 memb. ring HIS amber94_6 12.01000 ; CK sp2 C 5 memb.ring in purines amber94_7 12.01000 ; CM sp2 C pyrimidines in pos. 5 & 6 amber94_8 12.01000 ; CN sp2 C aromatic 5&6 memb.ring junct.(TRP) amber94_9 12.01000 ; CQ sp2 C in 5 mem.ring of purines between 2 N amber94_10 12.01000 ; CR sp2 arom as CQ but in HIS amber94_11 12.01000 ; CT sp3 aliphatic C amber94_12 12.01000 ; CV sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) amber94_13 12.01000 ; CW sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) amber94_14 12.01000 ; C* sp2 arom. 5 memb.ring w/1 subst. (TRP) amber94_15 40.08000 ; Ca2+ calcium amber94_16 19.00000 ; F fluorine amber94_17 1.00800 ; H H bonded to nitrogen atoms amber94_18 1.00800 ; HC H aliph. bond. to C without electrwd.group amber94_19 1.00800 ; H1 H aliph. bond. to C with 1 electrwd. group amber94_20 1.00800 ; H2 H aliph. bond. to C with 2 electrwd.groups amber94_21 1.00800 ; H3 H aliph. bond. to C with 3 eletrwd.groups amber94_22 1.00800 ; HA H arom. bond. to C without elctrwd. groups amber94_23 1.00800 ; H4 H arom. bond. to C with 1 electrwd. group amber94_24 1.00800 ; H5 H arom. bond. to C with 2 electrwd. groups amber94_25 1.00800 ; HO hydroxyl group amber94_26 1.00800 ; HS hydrogen bonded to sulphur amber94_27 1.00800 ; HW H in TIP3P water amber94_28 1.00800 ; HP H bonded to C next to positively charged gr amber94_29 126.90000 ; I iodine amber94_30 35.45000 ; Cl- amber94_31 22.99000 ; Na+ amber94_32 131.00000 ; IB 'big ion w/ waters' for vacuum (Na+, 6H2O) amber94_33 24.30000 ; Mg2+ magnesium amber94_34 14.01000 ; N sp2 nitrogen in amide groups amber94_35 14.01000 ; NA sp2 N in 5 memb.ring w/H atom (HIS) amber94_36 14.01000 ; NB sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) amber94_37 14.01000 ; NC sp2 N in 6 memb.ring w/LP (ADE,GUA) amber94_38 14.01000 ; N2 sp2 N in amino groups amber94_39 14.01000 ; N3 sp3 N for charged amino groups (Lys, etc) amber94_40 14.01000 ; N* sp2 N amber94_41 16.00000 ; O carbonyl group oxygen amber94_42 16.00000 ; OW oxygen in TIP3P water amber94_43 16.00000 ; OH oxygen in hydroxyl group amber94_44 16.00000 ; OS ether and ester oxygen amber94_45 16.00000 ; O2 carboxyl and phosphate group oxygen amber94_46 30.97000 ; P phosphate amber94_47 32.06000 ; S sulphur in disulfide linkage amber94_48 32.06000 ; SH sulphur in cystine amber94_49 63.55000 ; CU copper amber94_50 55.00000 ; FE iron amber94_51 39.10000 ; K+ potassium amber94_52 85.47000 ; Rb+ rubidium amber94_53 132.90000 ; Cs+ cesium amber94_54 15.99940 ; SPC Water OW amber94_55 1.00800 ; SPC Water HW ;amber94_54 9.95140 ; SPC Water OW heavy ;amber94_55 4.03200 ; SPC Water HW heavy amber94_56 6.94000 ; Li+ from parm94/96 amber94_57 65.40000 ; Zn2+ from parm99 amber94_58 87.62000 ; Sr2+ from Tinker/ponder amber94_59 137.33000 ; Ba2+ from Tinker/ponder amber94_60 1.00800 ; tip4pEW HW amber94_61 16.00000 ; tip4pEW OW amber94_62 1.00800 ; tip4p HW amber94_63 16.00000 ; tip4p OW amber94_64 1.00800 ; tip5p HW amber94_65 16.00000 ; tip5p OW amber94_66 4.03200 ; TIP3P HEAVY dummy water HW amber94_67 9.95200 ; TIP3P heavy dummy water OW MW 0.00000 ; Dummy mass for tip4p/5p water extra point charge MNH3 0.00000 ; Dummy mass in rigid tetraedrical NH3 group MNH2 0.00000 ; Dummy mass in rigid umbrella-shaped NH2 group MCH3A 0.00000 ; Dummy mass in rigid tetraedrical CH3 group MCH3B 0.00000 ; Dummy mass in rigid tetraedrical CH3 group