; ######################################################################## ; # # ; # ffAMBER ports for GROMACS 4.0.2, 4.0.3, & 4.04 - February 2008 # ; # Eric J. Sorin - CSU Long Beach, Dept. of Chem & Biochem # ; # With significant contributions from # ; # Sanghyun Park, Jory Z. Ruscio, and Erik Thompson # ; # Please cite: Sorin & Pande (2005). Biophys. J. 88(4), 2472-2493. # ; # For additional information, tools, and updates # ; # please consult http://chemistry.csulb.edu/ffamber/ # ; # # ; ######################################################################## amber99_1 79.90000 ; BR bromine amber99_2 12.01000 ; C sp2 C carbonyl group amber99_3 12.01000 ; CA sp2 C pure aromatic (benzene) amber99_4 12.01000 ; CB sp2 aromatic C, 5&6 membered ring junction amber99_5 12.01000 ; CC sp2 aromatic C, 5 memb. ring HIS amber99_6 12.01000 ; CK sp2 C 5 memb.ring in purines amber99_7 12.01000 ; CM sp2 C pyrimidines in pos. 5 & 6 amber99_8 12.01000 ; CN sp2 C aromatic 5&6 memb.ring junct.(TRP) amber99_9 12.01000 ; CQ sp2 C in 5 mem.ring of purines between 2 N amber99_10 12.01000 ; CR sp2 arom as CQ but in HIS amber99_11 12.01000 ; CT sp3 aliphatic C amber99_12 12.01000 ; CV sp2 arom. 5 memb.ring w/1 N and 1 H (HIS) amber99_13 12.01000 ; CW sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS) amber99_14 12.01000 ; C* sp2 arom. 5 memb.ring w/1 subst. (TRP) amber99_15 40.08000 ; Ca2+ calcium amber99_16 19.00000 ; F fluorine amber99_17 1.00800 ; H H bonded to nitrogen atoms amber99_18 1.00800 ; HC H aliph. bond. to C without electrwd.group amber99_19 1.00800 ; H1 H aliph. bond. to C with 1 electrwd. group amber99_20 1.00800 ; H2 H aliph. bond. to C with 2 electrwd.groups amber99_21 1.00800 ; H3 H aliph. bond. to C with 3 eletrwd.groups amber99_22 1.00800 ; HA H arom. bond. to C without elctrwd. groups amber99_23 1.00800 ; H4 H arom. bond. to C with 1 electrwd. group amber99_24 1.00800 ; H5 H arom. bond. to C with 2 electrwd. groups amber99_25 1.00800 ; HO hydroxyl group amber99_26 1.00800 ; HS hydrogen bonded to sulphur amber99_27 1.00800 ; HW H in TIP3P water amber99_28 1.00800 ; HP H bonded to C next to positively charged gr amber99_29 126.90000 ; I iodine amber99_30 35.45000 ; Cl- amber99_31 22.99000 ; Na+ amber99_32 131.00000 ; IB 'big ion w/ waters' for vacuum (Na+, 6H2O) amber99_33 24.30000 ; Mg2+ magnesium amber99_34 14.01000 ; N sp2 nitrogen in amide groups amber99_35 14.01000 ; NA sp2 N in 5 memb.ring w/H atom (HIS) amber99_36 14.01000 ; NB sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA) amber99_37 14.01000 ; NC sp2 N in 6 memb.ring w/LP (ADE,GUA) amber99_38 14.01000 ; N2 sp2 N in amino groups amber99_39 14.01000 ; N3 sp3 N for charged amino groups (Lys, etc) amber99_40 14.01000 ; N* sp2 N amber99_41 16.00000 ; O carbonyl group oxygen amber99_42 16.00000 ; OW oxygen in TIP3P water amber99_43 16.00000 ; OH oxygen in hydroxyl group amber99_44 16.00000 ; OS ether and ester oxygen amber99_45 16.00000 ; O2 carboxyl and phosphate group oxygen amber99_46 30.97000 ; P phosphate amber99_47 32.06000 ; S sulphur in disulfide linkage amber99_48 32.06000 ; SH sulphur in cystine amber99_49 63.55000 ; CU copper amber99_50 55.00000 ; FE iron amber99_51 39.10000 ; K+ potassium amber99_52 85.47000 ; Rb+ rubidium amber99_53 132.90000 ; Cs+ cesium amber99_54 15.99940 ; SPC Water OW amber99_55 1.00800 ; SPC Water HW ;amber99_54 9.95140 ; SPC Water OW heavy ;amber99_55 4.03200 ; SPC Water HW heavy amber99_56 6.94000 ; Li+ from parm94/96 amber99_57 65.40000 ; Zn2+ from parm99 amber99_58 87.62000 ; Sr2+ from Tinker/ponder amber99_59 137.33000 ; Ba2+ from Tinker/ponder amber99_60 1.00800 ; tip4pEW HW amber99_61 16.00000 ; tip4pEW OW amber99_62 1.00800 ; tip4p HW amber99_63 16.00000 ; tip4p OW amber99_64 1.00800 ; tip5p HW amber99_65 16.00000 ; tip5p OW amber99_66 4.03200 ; TIP3P HEAVY dummy water HW amber99_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