!
! xplor-nih nucleic acid parameter file, version 1.0
!
! This file is intended to work with the topology file nucleic-1.0.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 120.0
angle XH XCE XCB $kang 120.0
angle XH XCA XNC $kang 120.0
angle XH XCE XNS $kang 120.0
angle XH XCE XNB $kang 120.0
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
! 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 XH XCH XCH XH $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