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* Toppar stream file generated by Troy Wymore
* Leonard biochem 2015
* For use with protein param and top
*
read rtf card append
* Topologies generated by
* CHARMM General Force Field (CGenFF) program version 1.0.0
36 1
!MASS -1 H 1.00800 H ! polar H
MASS -1 NECA 14.00700 N ! carboxylated lys (KCX) nitrogen
default first none last none
PRES KCX -1.00 ! Patch for carboxylated lysine, ns
DELETE ATOM HZ2
DELETE ATOM HZ3
GROUP
ATOM CE CT2 0.060
ATOM HE1 HA 0.090
ATOM HE2 HA 0.090
ATOM NZ NECA -0.810
ATOM HZ1 H 0.300
ATOM CX CC 0.690
ATOM OQ1 OC -0.710
ATOM OQ2 OC -0.710
BOND NZ CX
BOND CX OQ1
BOND CX OQ2
IMPR CX NZ OQ1 OQ2
ACCEPTOR OQ1 CX
ACCEPTOR OQ2 CX
END
read param card flex append
* Parameters generated by troy Wymore
* Leonard Biochem 2015
*
ATOMS
MASS -1 NECA 14.00700 ! carboxylated lys (KCX) nitrogen
!MASS -1 HA 1.00800 ! polar H
!MASS -1 CT2 12.01100 ! carbon
!Bond parameters
BONDS
CT2 NECA 380.00 1.4300 ! ECA/KCX, init from NH1 CT1, fq matched, ns
H NECA 440.00 1.0280 ! ECA/KCX, init from NH1 H, fq matched, ns
CC NECA 320.00 1.4617 ! ECA/KCX, init from NH2 CC/NH1 C, fq matched, ns
HA CT2 309.000 1.1110 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
!Angle parameters
ANGLES
CT3 CT2 NECA 67.70 110.93 ! ECA/KCX, init from NH3 CT2 CT3, fq matched, ns
CT2 CT2 NECA 67.70 110.93 ! ECA/KCX, set to CT3 CT2 NECA, ns
HA CT2 NECA 51.50 107.50 ! ECA/KCX, init from NC2 CT2 HA, fq match ok, ns
CC NECA CT2 50.00 115.00 ! ECA/KCX, init from CT2 NH1 C, fq matched, ns
CT2 NECA H 60.00 110.00 ! ECA/KCX, init from H NH1 CT1, fq match ok, ns
CC NECA H 60.00 110.00 ! ECA/KCX, init from H NH1 CT2, fq match ok, ns
NECA CC OC 80.00 110.00 ! ECA/KCX, init from O C NH1, fq match ok, ns
HA CT2 CT2 26.500 110.10 22.53 2.17900 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
HA CT2 HA 35.500 109.00 5.40 1.80200 ! ALLOW ALI
! alkane update, adm jr., 3/2/92
!Torsional parameters
DIHEDRALS
HA CT2 CT3 HA 0.1600 3 0.00 ! ECA/KCX, init from X CT2 CT3 X , ns
HA CT3 CT2 NECA 0.0400 3 0.00 ! ECA/KCX, init from HA CT3 CT2 CA, fq matched, ns
CC NECA CT2 CT3 1.1000 1 180.00 ! ECA/KCX, Set from ParamIt:dihfit, ns
CC NECA CT2 CT3 0.2000 3 0.00 ! ECA/KCX, Set from ParamIt:dihfit, ns
CC NECA CT2 CT2 1.1000 1 180.00 ! ECA/KCX, Set from ParamIt:dihfit, ns
CC NECA CT2 CT2 0.2000 3 0.00 ! ECA/KCX, Set from ParamIt:dihfit, ns
H NECA CT2 HA 0.0000 1 0.00 ! ECA/KCX, init from HA CT3 NH1 H, ns
CC NECA CT2 HA 0.0000 1 0.00 ! ECA/KCX, init from HA CT2 NH1 C, ns
CT2 NECA CC OC 2.2000 2 180.00 ! ECA/KCX, Set from ParamIt:dihfit, ns
CT3 CT2 NECA H 0.2000 3 0.00 ! ECA/KCX, Set from ParamIt:dihfit, ns
CT2 CT2 NECA H 0.2000 3 0.00 ! ECA/KCX, Set to CT3 CT2 NECA H, ns
H NECA CC OC 1.9250 2 180.00 ! ECA/KCX, Set from ParamIt:dihfit, ns
!Improper
IMPROPERS
CC NECA OC OC 96.0000 0 0.0000 ! ECA/KCX, init from OC X X CC, ns
NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
! Non-bonded parameters, Lennard-Jones, epsilon, Rmin/2
NECA 0.000000 -0.200000 1.850000 ! ECA/KCX, N for ECA, ns
END
RETURN
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