{-k} {assign AMBER parm94.dat atom types Feb '96 C.I.Bayly } {based on atypes.pcp} {General atom definition} !H,He,Ne,Ar,Xe,Kr,Rn ? g ; Li,Ca,Mg,Fe,Zn,Co,Be,Mn,Mo ? Me ; {conjugated atom definition; any atom single bonded to sp2 or sp} g-sp2,sp ? conj * ; g&sp3(-sp2,sp)-sp2,sp ? twoconj * * ; {resonant atom definition} N,O,S&conj ? res ; sp,sp2 ? res ; {aromatic ring definitions} res~res~res~res~res~res~@1 ? ar6 ar6 ar6 ar6 ar6 ar6 ; res~res~res~res~res~@1 ? ar5 ar5 ar5 ar5 ar5 ; {any flat ring} ar5,ar6 ? ar ; {3-membered rings} g~g~g~@1 ? r3 r3 r3 ; {electronegative atom} N,O,F,S,Cl,Br ? elneg ; {amide nitrogen} N-C=O,S ? namide * * ; {carbonyl, imine group} H,g-C=O ? * conyl oonyl ; H,g-C!ar=N ? * conyl * ; {imine N set to type NB below} conyl(=oonyl)-O&x1 ? * Ocarbox Ocarbox ; {carboxylate carbon} g-O&X2&x2-g ? * Oether * ; {oxygen with two single bonds} {nitrogen groups} N&x3(~O&x1)~O&x1 ? Nitro Ocarbox Ocarbox ; {nitro group - tentative jan 1999 CIBayly} N&x3-S,P(~O&x1)~O&x1 ? Nsulfon * * * ; {sulfonamide-type N is pyramidal} N&x2&fcm1-S,P(~O&x1)~O&x1 ? Nsulfon * * * ; {sulfonamide-type N is pyramidal} {thiols, sulfides, sulfone, sulfoxides, sulfinic and sulfonic acids} H-S&x2-H ? * slfd * ; g-S&x2-g,H ? * slfd * ; C,N-S(~O)-C,N ? * shyp oonyl * ; C,N-S&X3(~O&X1)~O&X1 ? * shyp Ocarbox Ocarbox ; C,N-S&X4(~O&X1)(~O&X1)~O&X1 ? * shyp Ocarbox Ocarbox Ocarbox ; C,N-S&X4(~O&X1)(~O&X1)-O&X2 ? * shyp Ocarbox Ocarbox Oether ; g-S&X4(~O&X1)(~O&X1)-g ? * shyp Ocarbox Ocarbox * ; O&X2-S&X4(~O&X1)(~O&X1)-O&X2 ? Oether shyp Ocarbox Ocarbox Oether ; O&X2,C,N-S&X3(~O&X1)~O&X2 ? * shyp oonyl * ; g=S&X1 ? * sdouble ; {phosphates, phosphonates} P(=O) ? * oonyl ; {phosphone ?} P(~O&X1)(~O&X1) ? * Ocarbox Ocarbox ; { general -PO3 -2 } g-O-S,P ? * Oether * ; { ether link to P} {biphenyl-type bridgehead CP} ar6~ar6~ar6~ar6~ar6~C&ar6(~@1)-C&ar6~ar6~ar6~ar6~ar6~ar6~@7 ? . . . . . Cbiph Cbiph . . . . . ; ar5~ar5~ar5~ar5~C&ar5(~@1)-C&ar5~ar5~ar5~ar5~ar5~@6 ? . . . . Cbiph Cbiph . . . . ; {fused aromatic cycles: bridgehead CB} C&ar6~ar6~ar6~ar6~ar6~C&ar6(~@1)~ar6~ar6~ar6~ar6~@1 ? Cfused_ar . . . . Cfused_ar . . . . ; C&ar6~ar6~ar6~ar6~ar6~C&ar6(~@1)~ar5~ar5~ar5~@1 ? Cfused_ar . . . . Cfused_ar . . . ; * > DU ; {"I don't know"} g > gg ; {default} C&x4 > CT ; {aliphatic C} C&x4-C&x4-C&x4-@1 > CJ CJ CJ ; {cyclopropyl } C&x4-C&x4-g-@1 > CJ CJ * ; {epoxide-type C} C&sp > C2 ; {acetylene/nitrile C} C&sp2 > CM ; {non-aromatic C=x} C&ar6 > CA ; {6-ring aromatic carbons} C&ar5 > Cstar ; {5-ring aromatic carbons} Cfused_ar > CB ; {e.g. napthalene bridgehead} C&ar(-g&elneg&ar)=g&elneg&ar5 > CR * * ; {ar C in between 2 eleneg in ar5 } conyl > C ; {carbonyl carbon} Cbiph > CP ; {biphenyl bridgehead} N > Nu ; {the "I don't know" nitrogen} N&sp3 > N3 ; {regular sp3 N, not charged} N&ar > Nstar ; {sp2 N} g&sp2-N!ar-H > * N * ; {sp2 amino N} g&ar-N!ar > * N2 ; {sp2 amino N} {g&ar-N(-H,g)-H,g > * ND * * ; aniline-type N jan2002 CIBayly needs work} g&ar-Acy1-N(-!H)-!H > * N3 * * ; {disubst aniline-type N apr2005 CIBayly} g&ar-Acy1-N(-H,g)-g&ar > * N2 * * ; {more delocalized aniline-type N oct2004 CIBayly} Nsulfon > N3 ; {sulfonamide-type N is pyramidal. Ordered after aromatic amine} g&ar-N&ar(-H)-g > * NA * * ; {e.g. HIS C-NH-C} N(-H)-C=O,S > N * * * ; {explicitly reset amide N to type N} Nitro > N2 ; {nitro group - guess jan 1999 CIBayly} namide > N ; {amide N} C,N=N-g > * NB * ; {e.g. HIS C=N-C} C,N-Acy2-N-g,H > * NB * ; {e.g. Schiff base CIBayly 6Sept2000} N&x3-C!ar=N&x3 > N2 C N2 ; {amidine} N&x3(-H)-Acy2-C > N2 * C ; {protonated imine} g=N&ar6-g > * NC * ; {pyridine N} N&x4 > N3 ; {+ve tetrahedral N} N&x1#g > NL * ; {univalent triple-bonded N} N=N-C&x4-@1 > NJ NJ * ; {aziridine} O > Ou ; {the "I don't know" oxygen} oonyl > O ; {carbonyl oxygen} Ocarbox > O2 ; {carboxylate oxygen} Oether > OS ; {ether oxygen} N&ar-O&x1 > * OS ; {nitroso oxygen} N&x4-O&x1,fc0 > * OS ; {nitroso oxygen} g-O&fcm1 > * O2 ; {oxide ion assumed delocalized} C&x4-O&fcm1 > * OS ; {alkoxide ion} g-O&x2-H > * OH HO ; {hydroxyl O & H} H-O&x2-H > * OW * ; {water oxygen} S > Su ; {the "I don't know" sulfur} sdouble > SD ; {double-bonded monovalent sulfur} shyp > SO ; {hypervalent sulfur} slfd > S ; {sulfide sulfur} slfd-H > SH * ; {thiol sulfur} P > P ; {phosphorus} H > HC ; {default H} H-C&sp3 > HC * ; {aliphatic H} H-C&sp3 > HC * ; {aliphatic H} H-C&sp3-elneg > H1 * * ; {aliph H; 1 elneg grp} H-C&sp3(-elneg)-elneg > H2 * * * ; {aliph H; 2 elneg grp} H-C&sp3(-elneg)(-elneg)-elneg > H3 * * * * ; {aliph H; 3 elneg grp} H-N > H * ; {H attached to N} H-O > HO * ; {H attached to O} H-O&x2-H > HW * HW ; {water hydrogen} slfd-H > * HS ; {thiol hydrogen} H-C&sp2 > HA * ; {aromatic H} H-C&sp2~elneg > H4 * * ; {arom H; 1 elneg grp} H-C&sp2(-elneg)=elneg > H5 * * * ; {arom H; 2 elneg grp} H-C&sp3-g&fc1 > HP * * ; {H on CT adjacent to +ve chg.} H-O&x2-C&sp3-O&x2-H > HX * * * HX ; {acetal hydroxyl must have vdW rad else collapses into singularity} H-O&x2-C&sp3-N&sp3 > HX * * * ; {acetal hydroxyl must have vdW rad else collapses into singularity} F > F ; Cl > CL ; Cl&X0 > IM ; Br > BR ; I > I ; {test organics} { ar5 > ar5 ; ar6 > ar6 ; } Li > Li ; Na > IP ; K > K ; Rb > Rb ; Cs > Cs ; Ca > C0 ; Mg > MG ; Fe > FE ; Cu > CU ; { AMBER pathological case: partially unsaturated 5-membered heterocyc } g~g-N=C-g~@1 > * * * CR * ; { 5-ring unsat } { AMBER pathological specialties e.g. unsaturated 5-membered rings } {C&ar5=C&ar5-g&ar5=g&ar5-g&ar5-@1 > CW CC * * * ; 5-ring unsat but doesn't handle exocyclic ketones in 4th position} C&ar5=C&ar5-g&ar5~g&ar5-g&ar5-@1 > CW CC * * * ; { 5-ring unsat } C&ar5=C&ar5-C&ar5=C&ar5-g&ar5-@1 > CW CC CC CW * ; { 5-ring unsat } C&ar5=N&ar5-g&ar5~g&ar5~g&ar5-@1 > CR NB * * * ; { 5-ring unsat } {maybe redundant: C&ar5=C&ar5-C&ar5=C&ar5-g-@1 > CW CC CC CW * ; 5-ring unsat } N&ar5=C&ar5-C&ar5=N&ar5~g&ar5-@1 > NB CR CR NB * ; { 5-ring unsat } C&ar5=C&ar5-elneg&ar5=C&ar5-elneg&ar5-@1 > CW CC * CR * ; { histidine-like ring} { fused 5,6 unsat systems } C&ar5&ar6~C&ar5&ar6-C&ar5=C&ar5-g-@1 > CB CB CC CW * ; { normal 5,6-ring } C&ar5&ar6~C&ar5&ar6-elneg&ar5=C&ar5-elneg&ar5-@1 > CB CB * CR * ; { his-like } ;;