! ! xplor-nih nucleic acid parameter file, version 1.1 ! ! This file is intended to work with the topology file nucleic-1.1.top ! ! This is a re-named and fixed copy of the file parnah1er1_mod_new.inp ! ! We've created this new filename in order to eliminate confusion ! between the various parameter/topology combinations that ship ! with xplor-nih. It has version numbers, and will be updated ! along with the rest of the xplor-nih package. ! ! chemical types have been named such that mixed protein/nucleic acid ! refinements are possible. ! ! If you find errors, PLEASE let us know. ! remark NUCLEIC ACID PARAMETER FILE CREATION RUN remark >>>NO WARRANTY EXPRESSED OR IMPLIED<<< remark remark ALL HYDROGEN NUCLEIC ACID PARAMETER FILE. remark DERIVED FROM PARMDNA8. LN and MP 1984 remark H-bond wells made 0.5 kcal deeper to improve basepair energies 8/20/84/ln remark H stretch & bend constants from URACIL normal mode fit. remark Magnesium (fudge) and spermine included. remark all references to water removed, ATB, 3-JAN-85 remark ALL IMPROPERS force constants increased to 500 to remark ensure perfect planes and chirality: GMC 1987 remark DIHEDRAL force constants that keep purin rings parallel remark increased to 500 (MN 7-NOV-86) remark includes parameters for purine GMC 1987 remark included impropers for chirality from parallhdg.dna (CDS 2005/11/03) set echo=false mess=off end evaluate ($kbon = 1000) ! kcal / mol-A^2 evaluate ($kang = 500) ! kcal / mol-rad^2 evaluate ($kchi = 500) ! kcal / mol-rad^2 evaluate ($kmtyl = 500) evaluate ($kmene = 500) evaluate ($kback = 500) evaluate ($kssbon = 500) evaluate ($kx.sang = 500) evaluate ($kimpr = 500) ! kcal / mol-rad^2 evaluate ($kdih = 1) ! kcal / mol-rad^2 bond XH XNA $kbon 1.0100 ! URA bond XH XNS $kbon 1.0100 ! INFERENCE bond XH XNH3 $kbon 1.04 ! -"- AND DISTANCE FROM PARAM7 bond XH XOH2 $kbon 0.96 bond XH2 XN2 $kbon 1.0100 ! Infer. bond XHO XOH $kbon 0.9600 ! PARAM7 (IR stretch 3400 cm-1) bond XHO XOS $kbon 0.9600 bond XH XCE $kbon 1.09! CH R0 from RKR K from DEP opt. bond XH XCF $kbon 1.09 bond XH XC2 $kbon 1.09 bond XH XC3 $kbon 1.09 bond YH YC2 $kbon 1.09 bond XH XCH $kbon 1.09 bond XP XO2 $kbon 1.4800 ! DEP bond XP XOS $kbon 1.6100 ! DEP bond XP XOH $kbon 1.6100 ! Infer. bond XOS XC2 $kbon 1.4300 ! DEP bond XOS XCH $kbon 1.4300 ! Infer. bond XO XC $kbon 1.2290 ! URA bond XOH XC2 $kbon 1.4300 bond XOH XCH $kbon 1.4300 bond XC2 XCH $kbon 1.5250 bond YC2 XCH $kbon 1.5250 bond XC2 XC2 $kbon 1.5250 bond XCH XCH $kbon 1.5250 bond XC3 XCH $kbon 1.5250 bond XC3 XC2 $kbon 1.5250 ! DEP bond XCB XCB $kbon 1.3700 ! similar to CF=CF bond XCA XCB $kbon 1.4040 ! Infer. from URA bond XCE XCB $kbon 1.4040 ! Infer. from URA bond XC XCB $kbon 1.4190 bond XCF XC $kbon 1.4440 ! URA bond XCF XCA $kbon 1.4330 bond XCF XCF $kbon 1.3500 ! URA bond XC XCS $kbon 1.4440 bond XCS XC3 $kbon 1.5250 bond XCS XCF $kbon 1.3430 bond XNS XCH $kbon 1.4750 bond XNS XCB $kbon 1.3740 bond XNS XCE $kbon 1.3710 bond XNS XC $kbon 1.3830 bond XNS XCF $kbon 1.3650 bond XNC XCB $kbon 1.3540 bond XNC XCE $kbon 1.3240 bond XNC XCA $kbon 1.3390 bond XNC XC $kbon 1.3580 bond XN2 XCA $kbon 1.3330 bond XNB XCB $kbon 1.3910 bond XNB XCE $kbon 1.3040 bond XNA XCA $kbon 1.3810 bond XNA XC $kbon 1.3880 bond XNH2E XCH $kbon 1.49 ! FROM PARAM3 bond XBR XCS $kbon 1.880 angle XH XCE XNC $kang 115.45 !CDS 2007/12/03 see next comment angle XH XCE XCB $kang 120.0 angle XH XCA XNC $kang 120.0 angle XH XCE XNS $kang 123.05 !CDS 2007/12/03 updated to be angle XH XCE XNB $kang 123.05 ! consistant w/ planar base angle XH XCF XCA $kang 120.0 angle XH XCF XCF $kang 120.0 angle XH XCF XNS $kang 120.0 angle XH XCF XCS $kang 120.0 angle XH XCF XC $kang 120.0 angle XH XC3 XCS $kang 109.47 angle XH XC3 XCH $kang 109.47 angle XH XC3 XOS $kang 109.47 ! FOR DMP angle XH XC3 XH $kang 109.47 angle XH XCH XH $kang 109.47 angle XH XCH XC3 $kang 109.47 angle XH XCH XCH $kang 109.47 angle XH XCH XC2 $kang 109.47 angle XH XCH XOS $kang 109.47 angle XH XCH XOH $kang 109.47 angle XH XCH XNS $kang 109.47 angle XH XCH XNH2E $kang 109.47 angle XH XC2 XCH $kang 109.47 angle XH XC2 XC2 $kang 109.47 angle XH XC2 XC3 $kang 109.47 angle XH XC2 XOS $kang 109.47 angle XH XC2 XOH $kang 109.47 angle XH XC2 XH $kang 109.47 angle XP XOS XC2 $kang 120.5000 ! DEP angle XP XOS XC3 $kang 120.5000 ! Guess (inferred from P-OS-C2) /LN angle XCH XOS XCH $kang 109.7000 angle XP XOS XCH $kang 120.5000 angle XHO XOS XCH $kang 107.3000 angle XHO XOS XC2 $kang 107.3000 angle XHO XOH XCH $kang 107.3000 angle XHO XOH XC2 $kang 107.3000 angle XHO XOH XP $kang 107.3000 angle XOS XP XOS $kang 102.6000 ! DEP angle XOH XP XOS $kang 102.6000 angle XOS XP XO2 $kang 108.2300 ! DEP angle XOH XP XO2 $kang 108.2300 angle XO2 XP XO2 $kang 119.9000 ! DEP angle XC XNA XH $kang 116.5000 ! URA angle XC XNA XC $kang 126.4000 ! URA angle XCA XNA XH $kang 119.3000 ! Infer. angle XCA XNA XC $kang 125.2000 ! Infer. angle XCB XNB XCE $kang 103.8000 angle XCB XNC XCE $kang 111.0000 angle XCA XNC XCE $kang 118.6000 angle XCE XNC XCE $kang 118.6000 angle XC XNC XCA $kang 120.5000 angle XCA XNC XCB $kang 112.2000 angle XCA XN2 XH2 $kang 120.0000 angle XH2 XN2 XH2 $kang 120.0000 angle XCH XNS XCB $kang 125.8000 angle XCH XNS XCE $kang 128.8000 angle XCB XNS XCE $kang 105.4000 ! Infer. angle XC XNS XCH $kang 117.6000 angle XCF XNS XCH $kang 121.2000 angle XC XNS XCF $kang 121.6000 ! Infer. angle XC XNS XH $kang 119.3000 angle XCB XNS XH $kang 119.3000 angle XCE XNS XH $kang 119.3000 angle XCF XNS XH $kang 119.3000 angle XH XNH3 XH $kang 109.5 ! FROM PARAM7 angle XH XNH3 XC2 $kang 109.5 angle XC2 XNH3 XC2 $kang 109.5 angle XNS XC XO $kang 120.9000 angle XNA XC XO $kang 120.6000 angle XCB XC XO $kang 128.8000 angle XNC XC XO $kang 122.5000 angle XCF XC XO $kang 125.3000 angle XCS XC XO $kang 125.3000 angle XCF XC XNA $kang 114.1000 angle XCS XC XNA $kang 114.1000 angle XNS XC XNA $kang 115.4000 angle XCB XC XNA $kang 111.3000 angle XNS XC XNC $kang 118.6000 angle XN2 XCA XNB $kang 118.3000 angle XN2 XCA XNC $kang 119.8000 angle XCB XCA XNC $kang 117.3000 angle XCB XCE XNC $kang 117.3000 angle XCB XCA XN2 $kang 123.5000 angle XCF XCA XNC $kang 121.5000 angle XN2 XCA XCF $kang 120.1000 angle XNC XCA XNA $kang 123.3000 angle XN2 XCA XNA $kang 116.0000 angle XCB XCB XNS $kang 106.2000 angle XNC XCB XNS $kang 126.0000 angle XNC XCB XCB $kang 127.7000 angle XCA XCB XNB $kang 132.4000 angle XCE XCB XNB $kang 132.4000 angle XCA XCB XCB $kang 117.3000 angle XCE XCB XCB $kang 117.3000 angle XCB XCB XNB $kang 110.4000 angle XC XCB XNB $kang 130.0000 angle XC XCB XCB $kang 119.2000 angle XNC XCE XNC $kang 129.1000 angle XNB XCE XNS $kang 113.9000 angle XNS XCF XCF $kang 121.2000 angle XNA XCF XCF $kang 121.2000 ! URA angle XCA XCF XCF $kang 117.0000 ! DEP infer. angle XCS XCF XNS $kang 121.2000 angle XC XCF XCF $kang 120.7000 angle XC2 XCH XOS $kang 110.0 angle XC2 XCH XOH $kang 111.0000 angle XCH XCH XOH $kang 111.0000 angle XC2 XCH XCH $kang 114.7000 angle XCH XCH XCH $kang 102.9500 angle XCH XCH XOS $kang 108.1000 angle XC3 XCH XOS $kang 111.0000 angle XOS XCH XNS $kang 107.8000 angle XC2 XCH XNS $kang 114.2000 angle XCH XCH XNS $kang 114.2000 angle XC2 XCH XNH2E $kang 111.0000! GUESSED BY INFERENCE angle XCH XCH XNH2E $kang 111.0000! GUESSED BY INFERENCE angle XOS XCH XNH2E $kang 111.0000! GUESSED BY INFERENCE angle XC3 XCH XCH $kang 111.0000! ADDED WITHOUT CHECKING angle XOS XC2 XC3 $kang 111.0000 ! DEP angle XOS XC2 XCH $kang 112.0000 angle XOH XC2 XCH $kang 112.0000 angle XCH XC2 XCH $kang 102.700 angle XC2 XC2 XNH3 $kang 109.5 ! FROM PARAM7 angle XC2 XC2 XC2 $kang 110.0 ! FROM PARAM7 angle XC2 XC2 XC3 $kang 112.0 angle XC XCS XC3 $kang 119.7000 angle XC XCS XCF $kang 120.7000 angle XC3 XCS XCF $kang 119.7000 angle XBR XCS XCF $kang 119.7000 angle XBR XCS XCA $kang 119.7000 angle XCH XCH YC2 $kang 103.2 angle XCH YC2 XCH $kang 102.7 angle XOS XCH YC2 $kang 108.35 angle XNS XCH YC2 $kang 114.2 angle XH XCH YC2 $kang 109.47 angle YH YC2 YH $kang 109.47 angle YH YC2 XCH $kang 109.47 angle YC2 XCH XOH $kang 111.0000 dihedral X XC2 XCH X $kdih 3 0.0000 dihedral X YC2 XCH X $kdih 3 0.0000 dihedral X XC2 XC2 X $kdih 3 0.0000 ! PARAM7 dihedral X XCH XCH X $kdih 3 0.0000 dihedral X XCH XOS X $kdih 3 0.0000 dihedral X XCH XOH X $kdih 3 0.0000 dihedral X XC2 XOH X $kdih 3 0.0000 dihedral X XC2 XOS X $kdih 3 0.0000 dihedral X XOS XP X $kdih 3 0.0000 dihedral X XOH XP X $kdih 3 0.0000 dihedral X XCH XNS X $kdih 2 0.0000 dihedral X XC2 XNH3 X $kdih 3 0.0 !SPERMINE,E/BOND 3 BONDS !dihedral X XCA XN2 X $kdih 2 180.0000 !dihedral X XNS XCE X $kdih 2 180.0 !dihedral X XNS XCF X $kdih 2 180.0 !dihedral X XNC XCE X $kdih 2 180.0 !dihedral X XCF XCF X $kdih 2 180.0 dihedral X XCS XC3 X $kdih 3 0.0 ! METHYL E/3 PER BOND dihedral X XOS XC3 X $kdih 3 0.0 ! METHYL E/3 PER BOND ! "WILMA OLSON SUGAR MODEL": dihedral XOH XCH XCH XCH $kdih 2 0.0000 ! ONLY AS GAUCHE dihedral XC3 XCH XCH XOS $kdih 2 0.0 ! FOR C5' WHICH IS A C3 IN MODEL dihedral XOS XCH XCH XOS $kdih 2 0.0000 ! dihedral XOS XCH XCH XOS $kdih 3 0.0000 ! dihedral XOS XCH XCH XCH $kdih 2 0.0000 ! dihedral XOS XCH XCH XCH $kdih 3 0.0000 dihedral XOH XCH XCH XOS $kdih 2 0.0000 ! dihedral XOH XCH XCH XOS $kdih 3 0.0000 ! dihedral XOS XCH XC2 XCH $kdih 2 0.0000 ! dihedral XOS XCH XC2 XCH $kdih 3 0.0000 ! DECR from 1.4 dihedral XOS XCH YC2 XCH $kdih 2 0.0000 ! dihedral XOS XCH YC2 XCH $kdih 3 0.0000 ! DECR from 1.4 dihedral XOS XCH XCH XC2 $kdih 2 0.0000 ! DECR FROM 0.5 dihedral XOS XCH XCH XC2 $kdih 3 0.0000 ! decr from 1.4 dihedral XOS XCH XCH YC2 $kdih 2 0.0000 ! DECR FROM 0.5 dihedral XOS XCH XCH YC2 $kdih 3 0.0000 ! decr from 1.4 ! ! OUT OF THE SUGAR dihedral XOS XP XOS XC2 $kdih 3 0.0000 dihedral XOS XP XOS XC2 $kdih 2 0.0000 dihedral XOS XP XOS XC3 $kdih 3 0.0000 ! Added by inference dihedral XOS XP XOS XC3 $kdih 2 0.0000 ! Added by inference dihedral XOS XP XOS XCH $kdih 3 0.0000 dihedral XOS XP XOS XCH $kdih 2 0.0000 ! Keeping purine rings parallel (from PARAM6): improper XCE XCB XCB XNC $kimpr 0 180.00 improper XCE XCB XCB XCE $kimpr 0 180.00 improper XCE XCB XCB XCA $kimpr 0 180.00 improper XCE XCB XCB XNA $kimpr 0 180.00 improper XNC XCB XCB XNB $kimpr 0 180.00 improper XCA XCB XCB XNS $kimpr 0 180.00 improper XCE XCB XCB XNS $kimpr 0 180.00 improper XC XCB XCB XNS $kimpr 0 180.00 improper XH X X XCE $kimpr 0 0.0000 !added for h's in improper XH X X XCF $kimpr 0 0.0000 !base planes (GMC) improper XC2 X X XCH $kimpr 0 35.2600 improper XC3 X X XCH $kimpr 0 35.2600 ! ADDED WITHOUT CHECKING improper XOH X X XCH $kimpr 0 35.2600 improper XOS X X XCH $kimpr 0 35.2600 improper XCH XOS YC2 XNS $kimpr 0 35.2600 improper XCH XOS XC2 XNS $kimpr 0 35.2600 improper XCH XOS XCH XNS $kimpr 0 35.2600 improper XCH XOS XC2 XNH2E $kimpr 0 35.2600 improper XCH XOS XCH XNH2E $kimpr 0 35.2600 improper XH X X XNA $kimpr 0 0.0000 ! URA improper XH X X XNS $kimpr 0 0.0000 ! INFERENCE improper XH2 X X XN2 $kimpr 0 0.0000 improper XC X X XCB $kimpr 0 0.0000 ! PLANAR IMPROPERS FROM URA FIT improper XC X X XCS $kimpr 0 0.0000 ! (OR INFERRED FROM IT) improper XC X X XCF $kimpr 0 0.0000 improper XC X X XO $kimpr 0 0.0000 ! URA improper XC X X XNC $kimpr 0 0.0000 improper XC X X XNS $kimpr 0 0.0000 improper XCA X X XCB $kimpr 0 0.0000 improper XCA X X XNC $kimpr 0 0.0000 improper XCE X X XNC $kimpr 0 0.0000 improper XCA X X XN2 $kimpr 0 0.0000 improper XCA X X XNS $kimpr 0 0.0000 improper XCB X X XCE $kimpr 0 0.0000 improper XCB X X XNA $kimpr 0 0.0000 improper XCB X X XNB $kimpr 0 0.0000 improper XCB X X XNC $kimpr 0 0.0000 improper XCB X X XNS $kimpr 0 0.0000 improper XCF X X XNC $kimpr 0 0.0000 improper XCF X X XNA $kimpr 0 0.0000 improper XCH X X XNS $kimpr 0 0.0000 !increased from 40 improper XC3 X X XCS $kimpr 0 0.0000 !to 80 for planarity improper XNB X X XNS $kimpr 0 0.0000 improper XBR X X XCS $kimpr 0 0.0000 improper X XCA XN2 X $kimpr 2 180.0000 improper X XNS XCE X $kimpr 2 180.0 improper X XNS XCF X $kimpr 2 180.0 improper X XNC XCE X $kimpr 2 180.0 improper X XCF XCF X $kimpr 2 180.0 improper X XCA XH2 XH2 $kimpr 0 0.0 ! JJK 3/10/04 for holding iminos coplanar ! NEW IMPROPERS ADDED IN ORDER TO DEFINE THE CHIRALITY AT C1' ! C2' C3' AND C4'. ! added by Zeena Johar, 2004/09/22 !improper XH XCH XCH XOH $kimpr 0 63.4030 !improper XH XCH XCH XOS $kimpr 0 65.0000 !improper XH XC2 XCH XOS $kimpr 0 65.0000 !improper XH XOS XH XCH $kimpr 0 70.6690 !improper XH XCH XOS XNS $kimpr 0 -65.1610 ! chiral centers in the sugar ring improper XH XCH XOS XNS $kimpr 0 -65.0000 !c1' improper XH XC2 XOS XNS $kimpr 0 -65.0000 !added(dna),ATB improper XH YC2 XOS XNS $kimpr 0 -65.0000 !added(dna),ATB improper XH XCH XCH XOH $kimpr 0 65.0000 !c2' for RNA improper XH XCH XCH XOS $kimpr 0 65.0000 !c3' improper XH XCH XC2 XOH $kimpr 0 65.0000 !added(dna),ATB improper XH XCH YC2 XOH $kimpr 0 65.0000 !added(dna),ATB improper XH XCH XC2 XOS $kimpr 0 65.0000 !added(dna),ATB improper XH XCH YC2 XOS $kimpr 0 65.0000 !added(dna),ATB improper XH XC2 XCH XOS $kimpr 0 65.0000 !c4' {* chiral improper included for H5'/H5'' and H2'/H2'' def., according to *} {* Wijmenga, Mooren and Hilbers in NMR of nucl. acids, (Ed. Roberts) *} improper XH XOS XH XCH $kimpr 0 71.27 ! chirality around C5'. Value from bond/angle mini struct improper XH XOH XH XCH $kimpr 0 73 ! CDS - changed from 65 - this is used at the 5-terminus improper YH XCH XCH YH $kimpr 0 -60.27 ! chirality around DNA C2'. Val from bond/angle mini struct ! ! Added methyl chirality for thy to avoid "umbrella" methyls ! Setup of atom selections and parameter value taken from ! parallhdg_procheck.pro's alanine. ! ! JJK 3/9/04 ! improper XH XH XCS XH $kimpr 0 -66.514 ! Taken from Rossky Karplus and Rahman BIOPOLY (1979) ! 0.05 ADDED TO RADII TO IMPROVE ON NUCL.ACID STACKING/LN ! ! eps sigma eps(1:4) sigma(1:4) ! the radius is sigma*2^(-5/6) NONBonded XBR 0.8000 3.5636 0.8000 3.5636 NONBonded XC2 0.0900 3.2970 0.0900 3.2970 NONBonded YC2 0.0900 3.2970 0.0900 3.2970 NONBonded XCH 0.0900 3.2970 0.0900 3.2970 NONBonded XH 0.0045 2.6160 0.0045 2.6160 NONBonded YH 0.0045 2.6160 0.0045 2.6160 NONBonded XH2 0.0045 1.6040 0.0045 1.6040 ! ! give it the same as th Hn from RKR NONBonded XHO 0.0045 1.6040 0.0045 1.6040 NONBonded XMG 0.2000 2.8509 0.2000 2.8509 ! G U E S S ! ! THIS STILL IS AN EXTENDED ATOM NONBonded XNH2E 0.1600 3.0291 0.1600 3.0291 NONBonded XNH3 0.1600 2.8591 0.1600 2.8591 NONBonded XNS 0.1600 2.8591 0.1600 2.8591 NONBonded XO2 0.2304 2.7290 0.2304 2.7290 NONBonded XOH 0.2304 2.5508 0.2304 2.5508 NONBonded XOS 0.2304 2.7290 0.2304 2.7290 NONBonded XP 0.5849 3.3854 0.5849 3.3854 NONBonded XSD 0.3515 2.6727 0.3515 2.6727 ! G U E S S !BASES NONBonded XCA 0.0900 3.2970 0.0900 3.2970 NONBonded XCB 0.0900 3.2970 0.0900 3.2970 NONBonded XCE 0.0900 3.2970 0.0900 3.2970 NONBonded XCF 0.0900 3.2970 0.0900 3.2970 NONBonded XCS 0.0900 3.2970 0.0900 3.2970 NONBonded XC3 0.0900 3.2970 0.0900 3.2970 NONBonded XN2 0.1600 2.8591 0.1600 2.8591 NONBonded XNA 0.1600 2.8591 0.1600 2.8591 NONBonded XC 0.0900 3.2970 0.0900 3.2970 NONBonded XO 0.2304 2.7290 0.2304 2.7290 NONBonded XNC 0.1600 2.8591 0.1600 2.8591 NONBonded XNB 0.1600 2.8591 0.1600 2.8591 ! NOTE: the NBFIXES include aliphatic hydrogens !!!!!!!!! check !!! ! the following NBFIXes are for DNA-DNA hydrogen bonding ! terms ! ------1-4------ ! A B A B ! [Kcal/(mol A^12)] [Kcal/(mol A^6)] ! nbfix XHO XO 0.05 0.1 0.05 0.1 nbfix XHO XO2 0.05 0.1 0.05 0.1 nbfix XHO XOS 0.05 0.1 0.05 0.1 nbfix XHO XOH 0.05 0.1 0.05 0.1 nbfix XHO XNB 0.05 0.1 0.05 0.1 nbfix XHO XNC 0.05 0.1 0.05 0.1 nbfix XH XO 0.05 0.1 0.05 0.1 nbfix XH XO2 0.05 0.1 0.05 0.1 nbfix XH XOS 0.05 0.1 0.05 0.1 nbfix XH XOH 0.05 0.1 0.05 0.1 nbfix XH XNB 0.05 0.1 0.05 0.1 nbfix XH XNC 0.05 0.1 0.05 0.1 nbfix XH2 XO 0.05 0.1 0.05 0.1 nbfix XH2 XO2 0.05 0.1 0.05 0.1 nbfix XH2 XOS 0.05 0.1 0.05 0.1 nbfix XH2 XOH 0.05 0.1 0.05 0.1 nbfix XH2 XNB 0.05 0.1 0.05 0.1 nbfix XH2 XNC 0.05 0.1 0.05 0.1 AEXP=4 REXP=6 HAEX=4 AAEX=2 ! "all" possible combinations of HB-pairs in nucleic acids: ! WELL DEPTHS DEEPENED BY 0.5 KCAL TO IMPROVE BASEPAIR ENERGIES /LN ! AND DISTANCES INCREASED BY 0.05 hbond XN* XN* -3.5 3.05 hbond XN* XO* -4.0 2.95 hbond XO* XO* -4.75 2.80 hbond XO* XN* -4.50 2.90 set echo=$prev_echo mess=$prev_messages end