930 lines
42 KiB
Promela
930 lines
42 KiB
Promela
# This is a modified version of tinker's amber.prm
|
|
# with several corrections (?) which bring it into
|
|
# compliance with Amber's "parm96.dat"
|
|
|
|
##############################
|
|
## ##
|
|
## Force Field Definition ##
|
|
## ##
|
|
##############################
|
|
|
|
|
|
forcefield AMBER95
|
|
|
|
vdwtype LENNARD-JONES
|
|
radiusrule ARITHMETIC
|
|
radiustype R-MIN
|
|
radiussize RADIUS
|
|
epsilonrule GEOMETRIC
|
|
vdw-14-use
|
|
vdw-scale 2.0
|
|
chg-14-use
|
|
chg-scale 1.2
|
|
dielectric 1.0
|
|
|
|
|
|
#############################
|
|
## ##
|
|
## Literature References ##
|
|
## ##
|
|
#############################
|
|
|
|
|
|
W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, Jr.,
|
|
D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell and P. A. Kollman,
|
|
"A Second Generation Force Field for the Simulation of Proteins, Nucleic
|
|
Acids, and Organic Molecules", J. Am. Chem. Soc., 117, 5179-5197 (1995)
|
|
[PARM94]
|
|
|
|
P. Kollman, R. Dixon, W. Cornell, T. Fox, C. Chipot and A. Pohorille,
|
|
"The Development/Application of a 'Minimalist' Organic/Biochemical
|
|
Molecular Mechanic Force Field using a Combination of ab Initio
|
|
Calculations and Experimental Data", in Computer Simulation of
|
|
Biomolecular Systems, W. F. van Gunsteren, P. K. Weiner, A. J. Wilkinson,
|
|
eds., Volume 3, 83-96 (1997) [PARM96]
|
|
|
|
G. Moyna, H. J. Williams, R. J. Nachman and A. I. Scott, "Conformation in
|
|
Solution and Dynamics of a Structurally Constrained Linear Insect Kinin
|
|
Pentapeptide Analogue", Biopolymers, 49, 403-413 (1999) [AIB charges]
|
|
|
|
Current parameter values are available from the AMBER site in Peter
|
|
Kollman's lab at UCSF, http://www.amber.ucsf.edu/amber/amber.html/
|
|
|
|
|
|
#############################
|
|
## ##
|
|
## Atom Type Definitions ##
|
|
## ##
|
|
#############################
|
|
|
|
|
|
########################################################
|
|
## ##
|
|
## TINKER Atom Class Numbers to Amber-95 Atom Names ##
|
|
## ##
|
|
## 1 CT 11 CN 21 OW 31 HO ##
|
|
## 2 C 12 CK 22 OH 32 HS ##
|
|
## 3 CA 13 CQ 23 OS 33 HA ##
|
|
## 4 CM 14 N 24 O 34 HC ##
|
|
## 5 CC 15 NA 25 O2 35 H1 ##
|
|
## 6 CV 16 NB 26 S 36 H2 ##
|
|
## 7 CW 17 NC 27 SH 37 H3 ##
|
|
## 8 CR 18 N* 28 P 38 HP ##
|
|
## 9 CB 19 N2 29 H 39 H4 ##
|
|
## 10 C* 20 N3 30 HW 40 H5 ##
|
|
## ##
|
|
########################################################
|
|
|
|
|
|
atom 1 1 CT "Amber CT" 7 14.003 4
|
|
atom 2 2 C "Amber C" 6 12.000 3
|
|
atom 3 3 CA "Amber CA" 6 12.000 3
|
|
atom 4 4 CM "Amber CM" 1 1.008 3
|
|
atom 5 5 CC "Amber CC" 8 15.995 3
|
|
atom 6 6 CV "Amber CV" 1 1.008 3
|
|
atom 7 7 CW "Amber CW" 7 14.003 3
|
|
atom 8 8 CR "Amber CR" 6 12.000 3
|
|
atom 9 9 CB "Amber CB" 6 12.000 3
|
|
atom 10 10 C* "Amber C*" 1 1.008 3
|
|
atom 11 11 CN "Amber CN" 8 15.995 3
|
|
atom 12 12 CK "Amber CK" 1 1.008 3
|
|
atom 13 13 CQ "Amber CQ" 6 12.000 3
|
|
atom 14 14 N "Amber N" 1 1.008 3
|
|
atom 15 15 NA "Amber NA" 7 14.003 3
|
|
atom 16 16 NB "Amber NB" 6 12.000 2
|
|
atom 17 17 NC "Amber NC" 6 12.000 2
|
|
atom 18 18 N* "Amber N*" 1 1.008 2
|
|
atom 19 19 N2 "Amber N2" 8 15.995 3
|
|
atom 20 20 N3 "Amber N3" 1 1.008 4
|
|
atom 21 21 OW "Amber OW" 6 12.000 2
|
|
atom 22 22 OH "Amber OH" 1 1.008 2
|
|
atom 23 23 OS "Amber OS" 6 12.000 2
|
|
atom 24 24 O "Amber O" 1 1.008 1
|
|
atom 25 25 O2 "Amber O2" 7 14.003 1
|
|
atom 26 26 S "Amber S" 6 12.000 2
|
|
atom 27 27 SH "Amber SH" 6 12.000 2
|
|
atom 28 28 P "Amber P" 1 1.008 4
|
|
atom 29 29 H "Amber H" 8 15.995 1
|
|
atom 30 30 HW "Amber HW" 1 1.008 1
|
|
atom 31 31 HO "Amber HO" 6 12.000 1
|
|
atom 32 32 HS "Amber HS" 1 1.008 1
|
|
atom 33 33 HA "Amber HA" 6 12.000 1
|
|
atom 34 34 HC "Amber HC" 1 1.008 1
|
|
atom 35 35 H1 "Amber H1" 6 12.000 1
|
|
atom 36 36 H2 "Amber H2" 1 1.008 1
|
|
atom 37 37 H3 "Amber H3" 7 14.003 1
|
|
atom 38 38 HP "Amber HP" 6 12.000 1
|
|
atom 39 39 H4 "Amber H4" 6 12.000 1
|
|
atom 40 40 H5 "Amber H5" 6 12.000 1
|
|
|
|
################################
|
|
## ##
|
|
## Van der Waals Parameters ##
|
|
## ##
|
|
################################
|
|
|
|
|
|
vdw 1 1.9080 0.1094
|
|
vdw 2 1.9080 0.0860
|
|
vdw 3 1.9080 0.0860
|
|
vdw 4 1.9080 0.0860
|
|
vdw 5 1.9080 0.0860
|
|
vdw 6 1.9080 0.0860
|
|
vdw 7 1.9080 0.0860
|
|
vdw 8 1.9080 0.0860
|
|
vdw 9 1.9080 0.0860
|
|
vdw 10 1.9080 0.0860
|
|
vdw 11 1.9080 0.0860
|
|
vdw 12 1.9080 0.0860
|
|
vdw 13 1.9080 0.0860
|
|
vdw 14 1.8240 0.1700
|
|
vdw 15 1.8240 0.1700
|
|
vdw 16 1.8240 0.1700
|
|
vdw 17 1.8240 0.1700
|
|
vdw 18 1.8240 0.1700
|
|
vdw 19 1.8240 0.1700
|
|
vdw 20 1.8240 0.1700
|
|
vdw 21 1.7683 0.1520
|
|
vdw 22 1.7210 0.2104
|
|
vdw 23 1.6837 0.1700
|
|
vdw 24 1.6612 0.2100
|
|
vdw 25 1.6612 0.2100
|
|
vdw 26 2.0000 0.2500
|
|
vdw 27 2.0000 0.2500
|
|
vdw 28 2.1000 0.2000
|
|
vdw 29 0.6000 0.0157
|
|
vdw 30 0.0001 0.0000
|
|
vdw 31 0.0001 0.0000
|
|
vdw 32 0.6000 0.0157
|
|
vdw 33 1.4590 0.0150
|
|
vdw 34 1.4870 0.0157
|
|
vdw 35 1.3870 0.0157
|
|
vdw 36 1.2870 0.0157
|
|
vdw 37 1.1870 0.0157
|
|
vdw 38 1.1000 0.0157
|
|
vdw 39 1.4090 0.0150
|
|
vdw 40 1.3590 0.0150
|
|
|
|
|
|
##################################
|
|
## ##
|
|
## Bond Stretching Parameters ##
|
|
## ##
|
|
##################################
|
|
|
|
|
|
bond 1 1 310.0 1.5260
|
|
bond 1 2 317.0 1.5220
|
|
bond 1 3 317.0 1.5100
|
|
bond 1 4 317.0 1.5100
|
|
bond 1 5 317.0 1.5040
|
|
bond 1 10 317.0 1.4950
|
|
bond 1 14 337.0 1.4490
|
|
bond 1 18 337.0 1.4750
|
|
bond 1 19 337.0 1.4630
|
|
bond 1 20 367.0 1.4710
|
|
bond 1 22 320.0 1.4100
|
|
bond 1 23 320.0 1.4100
|
|
bond 1 26 227.0 1.8100
|
|
bond 1 27 237.0 1.8100
|
|
bond 1 34 340.0 1.0900
|
|
bond 1 35 340.0 1.0900
|
|
bond 1 36 340.0 1.0900
|
|
bond 1 37 340.0 1.0900
|
|
bond 1 38 340.0 1.0900
|
|
bond 2 3 469.0 1.4090
|
|
bond 2 4 410.0 1.4440
|
|
bond 2 9 447.0 1.4190
|
|
bond 2 14 490.0 1.3350
|
|
bond 2 15 418.0 1.3880
|
|
bond 2 17 457.0 1.3580
|
|
bond 2 18 424.0 1.3830
|
|
bond 2 22 450.0 1.3640
|
|
bond 2 24 570.0 1.2290
|
|
bond 2 25 656.0 1.2500
|
|
bond 3 3 469.0 1.4000
|
|
bond 3 4 427.0 1.4330
|
|
bond 3 9 469.0 1.4040
|
|
bond 3 11 469.0 1.4000
|
|
bond 3 15 427.0 1.3810
|
|
bond 3 17 483.0 1.3390
|
|
bond 3 19 481.0 1.3400
|
|
bond 3 33 367.0 1.0800
|
|
bond 3 39 367.0 1.0800
|
|
bond 4 4 549.0 1.3500
|
|
bond 4 18 448.0 1.3650
|
|
bond 4 33 367.0 1.0800
|
|
bond 4 39 367.0 1.0800
|
|
bond 4 40 367.0 1.0800
|
|
bond 5 6 512.0 1.3750
|
|
bond 5 7 518.0 1.3710
|
|
bond 5 15 422.0 1.3850
|
|
bond 5 16 410.0 1.3940
|
|
bond 6 16 410.0 1.3940
|
|
bond 6 39 367.0 1.0800
|
|
bond 7 10 546.0 1.3520
|
|
bond 7 15 427.0 1.3810
|
|
bond 7 39 367.0 1.0800
|
|
bond 8 15 477.0 1.3430
|
|
bond 8 16 488.0 1.3350
|
|
bond 8 40 367.0 1.0800
|
|
bond 9 9 520.0 1.3700
|
|
bond 9 10 388.0 1.4590
|
|
bond 9 11 447.0 1.4190
|
|
bond 9 16 414.0 1.3910
|
|
bond 9 17 461.0 1.3540
|
|
bond 9 18 436.0 1.3740
|
|
bond 10 34 367.0 1.0800
|
|
bond 11 15 428.0 1.3800
|
|
bond 12 16 529.0 1.3040
|
|
bond 12 18 440.0 1.3710
|
|
bond 12 40 367.0 1.0800
|
|
bond 13 17 502.0 1.3240
|
|
bond 13 40 367.0 1.0800
|
|
bond 14 29 434.0 1.0100
|
|
bond 15 29 434.0 1.0100
|
|
bond 18 29 434.0 1.0100
|
|
bond 19 29 434.0 1.0100
|
|
bond 20 29 434.0 1.0100
|
|
bond 21 30 553.0 0.9572
|
|
bond 22 28 230.0 1.6100
|
|
bond 22 31 553.0 0.9600
|
|
bond 23 28 230.0 1.6100
|
|
bond 23 31 553.0 0.9600
|
|
bond 25 28 525.0 1.4800
|
|
bond 26 26 166.0 2.0380
|
|
bond 27 32 274.0 1.3360
|
|
bond 30 30 553.0 1.5136
|
|
|
|
|
|
################################
|
|
## ##
|
|
## Angle Bending Parameters ##
|
|
## ##
|
|
################################
|
|
|
|
|
|
angle 1 1 1 40.00 109.50
|
|
angle 1 1 2 63.00 111.10
|
|
angle 1 1 3 63.00 114.00
|
|
angle 1 1 5 63.00 113.10
|
|
angle 1 1 10 63.00 115.60
|
|
angle 1 1 14 80.00 109.70
|
|
angle 1 1 18 50.00 109.50
|
|
angle 1 1 19 80.00 111.20
|
|
angle 1 1 20 80.00 111.20
|
|
angle 1 1 22 50.00 109.50
|
|
angle 1 1 23 50.00 109.50
|
|
angle 1 1 26 50.00 114.70
|
|
angle 1 1 27 50.00 108.60
|
|
angle 1 1 34 50.00 109.50
|
|
angle 1 1 35 50.00 109.50
|
|
angle 1 1 36 50.00 109.50
|
|
angle 1 1 38 50.00 109.50
|
|
angle 2 1 14 63.00 110.10
|
|
angle 2 1 20 80.00 111.20
|
|
angle 2 1 34 50.00 109.50
|
|
angle 2 1 35 50.00 109.50
|
|
angle 2 1 38 50.00 109.50
|
|
angle 3 1 34 50.00 109.50
|
|
angle 4 1 34 50.00 109.50
|
|
angle 5 1 34 50.00 109.50
|
|
angle 10 1 34 50.00 109.50
|
|
angle 14 1 35 50.00 109.50
|
|
angle 18 1 23 50.00 109.50
|
|
angle 18 1 35 50.00 109.50
|
|
angle 18 1 36 50.00 109.50
|
|
angle 19 1 35 50.00 109.50
|
|
angle 20 1 35 50.00 109.50
|
|
angle 20 1 38 50.00 109.50
|
|
angle 22 1 35 50.00 109.50
|
|
angle 23 1 35 50.00 109.50
|
|
angle 23 1 36 50.00 109.50
|
|
angle 26 1 35 50.00 109.50
|
|
angle 27 1 35 50.00 109.50
|
|
angle 34 1 34 35.00 109.50
|
|
angle 35 1 35 35.00 109.50
|
|
angle 36 1 36 35.00 109.50
|
|
angle 38 1 38 35.00 109.50
|
|
angle 1 2 14 70.00 116.60
|
|
angle 1 2 24 80.00 120.40
|
|
angle 1 2 25 70.00 117.00
|
|
angle 3 2 3 63.00 120.00
|
|
angle 3 2 22 70.00 120.00
|
|
angle 4 2 15 70.00 114.10
|
|
angle 4 2 24 80.00 125.30
|
|
angle 9 2 15 70.00 111.30
|
|
angle 9 2 24 80.00 128.80
|
|
angle 14 2 24 80.00 122.90
|
|
angle 15 2 18 70.00 115.40
|
|
angle 15 2 24 80.00 120.60
|
|
angle 17 2 18 70.00 118.60
|
|
angle 17 2 24 80.00 122.50
|
|
angle 18 2 24 80.00 120.90
|
|
angle 24 2 24 80.00 126.00
|
|
angle 25 2 25 80.00 126.00
|
|
angle 1 3 3 70.00 120.00
|
|
angle 2 3 3 63.00 120.00
|
|
angle 2 3 33 35.00 120.00
|
|
angle 3 3 3 63.00 120.00
|
|
angle 3 3 9 63.00 120.00
|
|
angle 3 3 11 63.00 120.00
|
|
angle 3 3 33 35.00 120.00
|
|
angle 3 3 39 35.00 120.00
|
|
angle 4 3 17 70.00 121.50
|
|
angle 4 3 19 70.00 120.10
|
|
angle 9 3 17 70.00 117.30
|
|
angle 9 3 19 70.00 123.50
|
|
angle 9 3 33 35.00 120.00
|
|
angle 9 3 39 35.00 120.00
|
|
angle 11 3 33 35.00 120.00
|
|
angle 15 3 17 70.00 123.30
|
|
angle 15 3 19 70.00 116.00
|
|
angle 17 3 19 70.00 119.30
|
|
angle 19 3 19 70.00 120.00
|
|
angle 1 4 2 70.00 119.70
|
|
angle 1 4 4 70.00 119.70
|
|
angle 2 4 4 63.00 120.70
|
|
angle 2 4 33 35.00 119.70
|
|
angle 2 4 39 35.00 119.70
|
|
angle 3 4 4 63.00 117.00
|
|
angle 3 4 33 35.00 123.30
|
|
angle 3 4 39 35.00 123.30
|
|
angle 4 4 18 70.00 121.20
|
|
angle 4 4 33 35.00 119.70
|
|
angle 4 4 39 35.00 119.70
|
|
angle 18 4 39 35.00 119.10
|
|
angle 1 5 6 70.00 120.00
|
|
angle 1 5 7 70.00 120.00
|
|
angle 1 5 15 70.00 120.00
|
|
angle 1 5 16 70.00 120.00
|
|
angle 6 5 15 70.00 120.00
|
|
angle 7 5 15 70.00 120.00
|
|
angle 7 5 16 70.00 120.00
|
|
angle 5 6 16 70.00 120.00
|
|
angle 5 6 39 35.00 120.00
|
|
angle 16 6 39 35.00 120.00
|
|
angle 5 7 15 70.00 120.00
|
|
angle 5 7 39 35.00 120.00
|
|
angle 10 7 15 70.00 108.70
|
|
angle 10 7 39 35.00 120.00
|
|
angle 15 7 39 35.00 120.00
|
|
angle 15 8 15 70.00 120.00
|
|
angle 15 8 16 70.00 120.00
|
|
angle 15 8 40 35.00 120.00
|
|
angle 16 8 40 35.00 120.00
|
|
angle 2 9 9 63.00 119.20
|
|
angle 2 9 16 70.00 130.00
|
|
angle 3 9 9 63.00 117.30
|
|
angle 3 9 10 63.00 134.90
|
|
angle 3 9 11 63.00 116.20
|
|
angle 3 9 16 70.00 132.40
|
|
angle 9 9 16 70.00 110.40
|
|
angle 9 9 17 70.00 127.70
|
|
angle 9 9 18 70.00 106.20
|
|
angle 10 9 11 63.00 108.80
|
|
angle 17 9 18 70.00 126.20
|
|
angle 1 10 7 70.00 125.00
|
|
angle 1 10 9 70.00 128.60
|
|
angle 7 10 9 63.00 106.40
|
|
angle 3 11 9 63.00 122.70
|
|
angle 3 11 15 70.00 132.80
|
|
angle 9 11 15 70.00 104.40
|
|
angle 16 12 18 70.00 113.90
|
|
angle 16 12 40 35.00 123.05
|
|
angle 18 12 40 35.00 123.05
|
|
angle 17 13 17 70.00 129.10
|
|
angle 17 13 40 35.00 115.45
|
|
angle 1 14 1 50.00 118.00
|
|
angle 1 14 2 50.00 121.90
|
|
angle 1 14 29 30.00 118.04
|
|
angle 2 14 29 30.00 120.00
|
|
angle 29 14 29 35.00 120.00
|
|
angle 2 15 2 70.00 126.40
|
|
angle 2 15 3 70.00 125.20
|
|
angle 2 15 29 30.00 116.80
|
|
angle 3 15 29 30.00 118.00
|
|
angle 5 15 8 70.00 120.00
|
|
angle 5 15 29 30.00 120.00
|
|
angle 7 15 8 70.00 120.00
|
|
angle 7 15 11 70.00 111.60
|
|
angle 7 15 29 30.00 120.00
|
|
angle 8 15 29 30.00 120.00
|
|
angle 11 15 29 30.00 123.10
|
|
angle 5 16 8 70.00 117.00
|
|
angle 6 16 8 70.00 117.00
|
|
angle 9 16 12 70.00 103.80
|
|
angle 2 17 3 70.00 120.50
|
|
angle 3 17 9 70.00 112.20
|
|
angle 3 17 13 70.00 118.60
|
|
angle 9 17 13 70.00 111.00
|
|
angle 1 18 2 70.00 117.60
|
|
angle 1 18 4 70.00 121.20
|
|
angle 1 18 9 70.00 125.80
|
|
angle 1 18 12 70.00 128.80
|
|
angle 2 18 4 70.00 121.60
|
|
angle 2 18 29 30.00 119.20
|
|
angle 4 18 29 30.00 121.20
|
|
angle 9 18 12 70.00 105.40
|
|
angle 9 18 29 30.00 125.80
|
|
angle 12 18 29 30.00 128.80
|
|
angle 1 19 3 50.00 123.20
|
|
angle 1 19 29 35.00 118.40
|
|
angle 3 19 29 35.00 120.00
|
|
angle 29 19 29 35.00 120.00
|
|
angle 1 20 1 50.00 109.50
|
|
angle 1 20 29 50.00 109.50
|
|
angle 29 20 29 35.00 109.50
|
|
angle 30 21 30 100.00 104.52
|
|
angle 1 22 31 55.00 108.50
|
|
angle 2 22 31 35.00 113.00
|
|
angle 28 22 31 45.00 108.50
|
|
angle 1 23 1 60.00 109.50
|
|
angle 1 23 28 100.00 120.50
|
|
angle 28 23 28 100.00 120.50
|
|
angle 1 26 1 62.00 98.90
|
|
angle 1 26 26 68.00 103.70
|
|
angle 1 27 32 43.00 96.00
|
|
angle 32 27 32 35.00 92.07
|
|
angle 22 28 23 45.00 102.60
|
|
angle 22 28 25 45.00 108.23
|
|
angle 23 28 23 45.00 102.60
|
|
angle 23 28 25 100.00 108.23
|
|
angle 25 28 25 140.00 119.90
|
|
angle 21 30 30 0.00 127.74
|
|
|
|
|
|
#####################################
|
|
## ##
|
|
## Improper Torsional Parameters ##
|
|
## ##
|
|
#####################################
|
|
|
|
|
|
imptors 3 3 2 22 1.100 180.0 2
|
|
imptors 1 14 2 24 10.500 180.0 2
|
|
imptors 1 25 2 25 10.500 180.0 2
|
|
imptors 3 3 3 1 1.100 180.0 2
|
|
imptors 3 2 3 33 1.100 180.0 2
|
|
imptors 3 3 3 33 1.100 180.0 2
|
|
imptors 11 3 3 33 1.100 180.0 2
|
|
imptors 3 9 3 33 1.100 180.0 2
|
|
imptors 19 19 3 19 10.500 180.0 2
|
|
imptors 15 6 5 1 1.100 180.0 2
|
|
imptors 15 7 5 1 1.100 180.0 2
|
|
imptors 16 7 5 1 1.100 180.0 2
|
|
imptors 5 16 6 39 1.100 180.0 2
|
|
imptors 5 15 7 39 1.100 180.0 2
|
|
imptors 10 15 7 39 1.100 180.0 2
|
|
imptors 15 15 8 40 1.100 180.0 2
|
|
imptors 16 15 8 40 1.100 180.0 2
|
|
imptors 15 16 8 40 1.100 180.0 2
|
|
imptors 7 9 10 1 1.100 180.0 2
|
|
imptors 2 1 14 1 1.000 180.0 2
|
|
imptors 2 1 14 29 1.000 180.0 2
|
|
imptors 2 29 14 29 1.000 180.0 2
|
|
imptors 8 7 15 29 1.000 180.0 2
|
|
imptors 5 8 15 29 1.000 180.0 2
|
|
imptors 7 11 15 29 1.000 180.0 2
|
|
imptors 1 3 19 29 1.000 180.0 2
|
|
imptors 3 29 19 29 1.000 180.0 2
|
|
|
|
|
|
############################
|
|
## ##
|
|
## Torsional Parameters ##
|
|
## ##
|
|
############################
|
|
|
|
|
|
###############################################################
|
|
## ##
|
|
## There are two AMBER95 parameterizations for the Cornell ##
|
|
## force field, PARM94 and PARM96. They differ only in the ##
|
|
## torsional parameters for peptide phi and psi rotations. ##
|
|
## ##
|
|
## PARM94 ##
|
|
## ##
|
|
## 14 1 2 14 0.75 180 1 1.35 180 2 0.40 180 4 ##
|
|
## 2 1 14 2 0.20 180 2 ##
|
|
## ##
|
|
## PARM96 ##
|
|
## ##
|
|
## 14 1 2 14 0.85 0 1 0.30 180 2 ##
|
|
## 2 1 14 2 0.85 0 1 0.30 180 2 ##
|
|
## ##
|
|
###############################################################
|
|
|
|
|
|
torsion 1 1 1 1 0.156 0.0 3
|
|
torsion 1 1 1 2 0.156 0.0 3
|
|
torsion 1 1 1 14 0.156 0.0 3
|
|
torsion 1 1 1 19 0.156 0.0 3
|
|
torsion 1 1 1 20 0.156 0.0 3
|
|
torsion 1 1 1 26 0.156 0.0 3
|
|
torsion 1 1 1 34 0.156 0.0 3
|
|
torsion 1 1 1 35 0.156 0.0 3
|
|
torsion 1 1 1 38 0.156 0.0 3
|
|
torsion 2 1 1 2 0.156 0.0 3
|
|
torsion 2 1 1 3 0.156 0.0 3
|
|
torsion 2 1 1 5 0.156 0.0 3
|
|
torsion 2 1 1 10 0.156 0.0 3
|
|
torsion 2 1 1 14 0.156 0.0 3
|
|
torsion 2 1 1 20 0.156 0.0 3
|
|
torsion 2 1 1 22 0.156 0.0 3
|
|
torsion 2 1 1 26 0.156 0.0 3
|
|
torsion 2 1 1 27 0.156 0.0 3
|
|
torsion 2 1 1 34 0.156 0.0 3
|
|
torsion 2 1 1 35 0.156 0.0 3
|
|
torsion 2 1 1 38 0.156 0.0 3
|
|
torsion 3 1 1 14 0.156 0.0 3
|
|
torsion 3 1 1 20 0.156 0.0 3
|
|
torsion 3 1 1 35 0.156 0.0 3
|
|
torsion 3 1 1 38 0.156 0.0 3
|
|
torsion 5 1 1 14 0.156 0.0 3
|
|
torsion 5 1 1 20 0.156 0.0 3
|
|
torsion 5 1 1 35 0.156 0.0 3
|
|
torsion 5 1 1 38 0.156 0.0 3
|
|
torsion 10 1 1 14 0.156 0.0 3
|
|
torsion 10 1 1 20 0.156 0.0 3
|
|
torsion 10 1 1 35 0.156 0.0 3
|
|
torsion 10 1 1 38 0.156 0.0 3
|
|
torsion 14 1 1 22 0.156 0.0 3
|
|
torsion 14 1 1 26 0.156 0.0 3
|
|
torsion 14 1 1 27 0.156 0.0 3
|
|
torsion 14 1 1 34 0.156 0.0 3
|
|
torsion 14 1 1 35 0.156 0.0 3
|
|
torsion 19 1 1 34 0.156 0.0 3
|
|
torsion 20 1 1 22 0.156 0.0 3
|
|
torsion 20 1 1 26 0.156 0.0 3
|
|
torsion 20 1 1 27 0.156 0.0 3
|
|
torsion 20 1 1 34 0.156 0.0 3
|
|
torsion 20 1 1 35 0.156 0.0 3
|
|
torsion 22 1 1 34 0.156 0.0 3
|
|
torsion 22 1 1 35 0.156 0.0 3
|
|
torsion 22 1 1 38 0.156 0.0 3
|
|
torsion 26 1 1 34 0.156 0.0 3
|
|
torsion 26 1 1 35 0.156 0.0 3
|
|
torsion 26 1 1 38 0.156 0.0 3
|
|
torsion 27 1 1 35 0.156 0.0 3
|
|
torsion 27 1 1 38 0.156 0.0 3
|
|
torsion 34 1 1 34 0.156 0.0 3
|
|
torsion 34 1 1 35 0.156 0.0 3
|
|
torsion 34 1 1 38 0.156 0.0 3
|
|
torsion 35 1 1 35 0.156 0.0 3
|
|
torsion 35 1 1 38 0.156 0.0 3
|
|
torsion 1 1 2 14 0.070 0.0 2 0.100 0.0 4
|
|
torsion 1 1 2 24 0.000 0.0 2
|
|
torsion 1 1 2 25 0.000 0.0 2
|
|
#torsion 14 1 2 14 0.750 180.0 1 1.350 180.0 2 0.400 180.0 4
|
|
torsion 14 1 2 14 0.850 0.0 1 0.300 180.0 2
|
|
torsion 14 1 2 24 0.000 0.0 2
|
|
torsion 14 1 2 25 0.000 0.0 2
|
|
torsion 20 1 2 14 0.000 0.0 2
|
|
torsion 20 1 2 24 0.000 0.0 2
|
|
torsion 34 1 2 14 0.000 0.0 2
|
|
torsion 34 1 2 24 0.000 0.0 2
|
|
torsion 34 1 2 25 0.000 0.0 2
|
|
torsion 35 1 2 14 0.000 0.0 2
|
|
torsion 35 1 2 24 0.000 0.0 2
|
|
torsion 35 1 2 25 0.000 0.0 2
|
|
torsion 38 1 2 14 0.000 0.0 2
|
|
torsion 38 1 2 24 0.000 0.0 2
|
|
torsion 1 1 3 3 0.000 0.0 2
|
|
torsion 34 1 3 3 0.000 0.0 2
|
|
torsion 1 1 5 6 0.000 0.0 2
|
|
torsion 1 1 5 7 0.000 0.0 2
|
|
torsion 1 1 5 15 0.000 0.0 2
|
|
torsion 1 1 5 16 0.000 0.0 2
|
|
torsion 34 1 5 6 0.000 0.0 2
|
|
torsion 34 1 5 7 0.000 0.0 2
|
|
torsion 34 1 5 15 0.000 0.0 2
|
|
torsion 34 1 5 16 0.000 0.0 2
|
|
torsion 1 1 10 7 0.000 0.0 2
|
|
torsion 1 1 10 9 0.000 0.0 2
|
|
torsion 34 1 10 7 0.000 0.0 2
|
|
torsion 34 1 10 9 0.000 0.0 2
|
|
torsion 1 1 14 1 0.000 0.0 2
|
|
torsion 1 1 14 2 0.530 0.0 1 0.150 180.0 3 0.500 180.0 4
|
|
torsion 1 1 14 29 0.000 0.0 2
|
|
torsion 2 1 14 1 0.000 0.0 2
|
|
#torsion 2 1 14 2 0.200 180.0 2
|
|
torsion 2 1 14 2 0.850 0.0 1 0.300 180.0 2
|
|
torsion 2 1 14 29 0.000 0.0 2
|
|
torsion 35 1 14 1 0.000 0.0 2
|
|
torsion 35 1 14 2 0.000 0.0 2
|
|
torsion 35 1 14 29 0.000 0.0 2
|
|
torsion 1 1 19 3 0.000 0.0 3
|
|
torsion 1 1 19 29 0.000 0.0 3
|
|
torsion 35 1 19 3 0.000 0.0 3
|
|
torsion 35 1 19 29 0.000 0.0 3
|
|
torsion 1 1 20 1 0.156 0.0 3
|
|
torsion 1 1 20 29 0.156 0.0 3
|
|
torsion 2 1 20 1 0.156 0.0 3
|
|
torsion 2 1 20 29 0.156 0.0 3
|
|
torsion 35 1 20 1 0.156 0.0 3
|
|
torsion 35 1 20 29 0.156 0.0 3
|
|
torsion 38 1 20 1 0.156 0.0 3
|
|
torsion 38 1 20 29 0.156 0.0 3
|
|
torsion 1 1 22 31 0.167 0.0 3
|
|
torsion 35 1 22 31 0.167 0.0 3
|
|
torsion 1 1 26 1 0.333 0.0 3
|
|
torsion 1 1 26 26 0.333 0.0 3
|
|
torsion 35 1 26 1 0.333 0.0 3
|
|
torsion 35 1 26 26 0.333 0.0 3
|
|
torsion 1 1 27 32 0.250 0.0 3
|
|
torsion 35 1 27 32 0.250 0.0 3
|
|
torsion 3 2 3 3 3.625 180.0 2
|
|
torsion 3 2 3 33 3.625 180.0 2
|
|
torsion 22 2 3 3 3.625 180.0 2
|
|
torsion 22 2 3 33 3.625 180.0 2
|
|
torsion 1 2 14 1 2.500 180.0 2
|
|
torsion 1 2 14 29 2.500 180.0 2
|
|
torsion 24 2 14 1 2.500 180.0 2
|
|
torsion 24 2 14 29 2.000 0.0 1 2.500 180.0 2
|
|
torsion 3 2 22 31 0.900 180.0 2
|
|
torsion 1 3 3 3 3.625 180.0 2
|
|
torsion 1 3 3 33 3.625 180.0 2
|
|
torsion 2 3 3 3 3.625 180.0 2
|
|
torsion 2 3 3 33 3.625 180.0 2
|
|
torsion 3 3 3 3 3.625 180.0 2
|
|
torsion 3 3 3 9 3.625 180.0 2
|
|
torsion 3 3 3 11 3.625 180.0 2
|
|
torsion 3 3 3 33 3.625 180.0 2
|
|
torsion 9 3 3 33 3.625 180.0 2
|
|
torsion 11 3 3 33 3.625 180.0 2
|
|
torsion 33 3 3 33 3.625 180.0 2
|
|
torsion 3 3 9 10 3.500 180.0 2
|
|
torsion 3 3 9 11 3.500 180.0 2
|
|
torsion 33 3 9 10 3.500 180.0 2
|
|
torsion 33 3 9 11 3.500 180.0 2
|
|
torsion 3 3 11 9 3.625 180.0 2
|
|
torsion 3 3 11 15 3.625 180.0 2
|
|
torsion 33 3 11 9 3.625 180.0 2
|
|
torsion 33 3 11 15 3.625 180.0 2
|
|
torsion 19 3 19 1 2.400 180.0 2
|
|
torsion 19 3 19 29 2.400 180.0 2
|
|
torsion 1 5 6 16 5.150 180.0 2
|
|
torsion 1 5 6 39 5.150 180.0 2
|
|
torsion 15 5 6 16 5.150 180.0 2
|
|
torsion 15 5 6 39 5.150 180.0 2
|
|
torsion 1 5 7 15 5.375 180.0 2
|
|
torsion 1 5 7 39 5.375 180.0 2
|
|
torsion 15 5 7 15 5.375 180.0 2
|
|
torsion 15 5 7 39 5.375 180.0 2
|
|
torsion 16 5 7 15 5.375 180.0 2
|
|
torsion 16 5 7 39 5.375 180.0 2
|
|
torsion 1 5 15 8 1.400 180.0 2
|
|
torsion 1 5 15 29 1.400 180.0 2
|
|
torsion 6 5 15 8 1.400 180.0 2
|
|
torsion 6 5 15 29 1.400 180.0 2
|
|
torsion 7 5 15 8 1.400 180.0 2
|
|
torsion 7 5 15 29 1.400 180.0 2
|
|
torsion 1 5 16 8 2.400 180.0 2
|
|
torsion 7 5 16 8 2.400 180.0 2
|
|
torsion 5 6 16 8 2.400 180.0 2
|
|
torsion 39 6 16 8 2.400 180.0 2
|
|
torsion 15 7 10 1 6.525 180.0 2
|
|
torsion 15 7 10 9 6.525 180.0 2
|
|
torsion 39 7 10 1 6.525 180.0 2
|
|
torsion 39 7 10 9 6.525 180.0 2
|
|
torsion 5 7 15 8 1.500 180.0 2
|
|
torsion 5 7 15 29 1.500 180.0 2
|
|
torsion 10 7 15 11 1.500 180.0 2
|
|
torsion 10 7 15 29 1.500 180.0 2
|
|
torsion 39 7 15 8 1.500 180.0 2
|
|
torsion 39 7 15 11 1.500 180.0 2
|
|
torsion 39 7 15 29 1.500 180.0 2
|
|
torsion 15 8 15 5 2.325 180.0 2
|
|
torsion 15 8 15 7 2.325 180.0 2
|
|
torsion 15 8 15 29 2.325 180.0 2
|
|
torsion 16 8 15 5 2.325 180.0 2
|
|
torsion 16 8 15 7 2.325 180.0 2
|
|
torsion 16 8 15 29 2.325 180.0 2
|
|
torsion 40 8 15 5 2.325 180.0 2
|
|
torsion 40 8 15 7 2.325 180.0 2
|
|
torsion 40 8 15 29 2.325 180.0 2
|
|
torsion 15 8 16 5 5.000 180.0 2
|
|
torsion 40 8 16 5 5.000 180.0 2
|
|
torsion 15 8 16 6 5.000 180.0 2
|
|
torsion 40 8 16 6 5.000 180.0 2
|
|
torsion 3 9 10 1 1.675 180.0 2
|
|
torsion 3 9 10 7 1.675 180.0 2
|
|
torsion 11 9 10 1 1.675 180.0 2
|
|
torsion 11 9 10 7 1.675 180.0 2
|
|
torsion 3 9 11 3 3.000 180.0 2
|
|
torsion 3 9 11 15 3.000 180.0 2
|
|
torsion 10 9 11 3 3.000 180.0 2
|
|
torsion 10 9 11 15 3.000 180.0 2
|
|
torsion 3 11 15 7 1.525 180.0 2
|
|
torsion 3 11 15 29 1.525 180.0 2
|
|
torsion 9 11 15 7 1.525 180.0 2
|
|
torsion 9 11 15 29 1.525 180.0 2
|
|
torsion 1 26 26 1 3.500 0.0 2 0.600 0.0 3
|
|
|
|
|
|
########################################
|
|
## ##
|
|
## Atomic Partial Charge Parameters ##
|
|
## ##
|
|
########################################
|
|
|
|
|
|
charge 1 0.0000
|
|
charge 2 0.0000
|
|
charge 3 0.0000
|
|
charge 4 0.0000
|
|
charge 5 0.0000
|
|
charge 6 0.0000
|
|
charge 7 0.0000
|
|
charge 8 0.0000
|
|
charge 9 0.0000
|
|
charge 10 0.0000
|
|
charge 11 0.0000
|
|
charge 12 0.0000
|
|
charge 13 0.0000
|
|
charge 14 0.0000
|
|
charge 15 0.0000
|
|
charge 16 0.0000
|
|
charge 17 0.0000
|
|
charge 18 0.0000
|
|
charge 19 0.0000
|
|
charge 20 0.0000
|
|
charge 21 0.0000
|
|
charge 22 0.0000
|
|
charge 23 0.0000
|
|
charge 24 0.0000
|
|
charge 25 0.0000
|
|
charge 26 0.0000
|
|
charge 27 0.0000
|
|
charge 28 0.0000
|
|
charge 29 0.0000
|
|
charge 30 0.0000
|
|
charge 31 0.0000
|
|
charge 32 0.0000
|
|
charge 33 0.0000
|
|
charge 34 0.0000
|
|
charge 35 0.0000
|
|
charge 36 0.0000
|
|
charge 37 0.0000
|
|
charge 38 0.0000
|
|
charge 39 0.0000
|
|
charge 40 0.0000
|
|
|
|
|
|
########################################
|
|
## ##
|
|
## Biopolymer Atom Type Conversions ##
|
|
## ##
|
|
########################################
|
|
|
|
biotype 1 CT "Amber CT" 1
|
|
biotype 2 C "Amber C" 2
|
|
biotype 3 CA "Amber CA" 3
|
|
biotype 4 CM "Amber CM" 4
|
|
biotype 5 CC "Amber CC" 5
|
|
biotype 6 CV "Amber CV" 6
|
|
biotype 7 CW "Amber CW" 7
|
|
biotype 8 CR "Amber CR" 8
|
|
biotype 9 CB "Amber CB" 9
|
|
biotype 10 C* "Amber C*" 10
|
|
biotype 11 CN "Amber CN" 11
|
|
biotype 12 CK "Amber CK" 12
|
|
biotype 13 CQ "Amber CQ" 13
|
|
biotype 14 N "Amber N" 14
|
|
biotype 15 NA "Amber NA" 15
|
|
biotype 16 NB "Amber NB" 16
|
|
biotype 17 NC "Amber NC" 17
|
|
biotype 18 N* "Amber N*" 18
|
|
biotype 19 N2 "Amber N2" 19
|
|
biotype 20 N3 "Amber N3" 20
|
|
biotype 21 OW "Amber OW" 21
|
|
biotype 22 OH "Amber OH" 22
|
|
biotype 23 OS "Amber OS" 23
|
|
biotype 24 O "Amber O" 24
|
|
biotype 25 O2 "Amber O2" 25
|
|
biotype 26 S "Amber S" 26
|
|
biotype 27 SH "Amber SH" 27
|
|
biotype 28 P "Amber P" 28
|
|
biotype 29 H "Amber H" 29
|
|
biotype 30 HW "Amber HW" 30
|
|
biotype 31 HO "Amber HO" 31
|
|
biotype 32 HS "Amber HS" 32
|
|
biotype 33 HA "Amber HA" 33
|
|
biotype 34 HC "Amber HC" 34
|
|
biotype 35 H1 "Amber H1" 35
|
|
biotype 36 H2 "Amber H2" 36
|
|
biotype 37 H3 "Amber H3" 37
|
|
biotype 38 HP "Amber HP" 38
|
|
biotype 39 H4 "Amber H4" 39
|
|
biotype 40 H5 "Amber H5" 40
|
|
|
|
############################8
|
|
## ##
|
|
## Literature References ##
|
|
## ##
|
|
#############################
|
|
|
|
|
|
W. S. Ross and C. C. Hardin, "Ion-Induced Stabilization of the G-DNA
|
|
Quadruplex: Free Energy Perturbation Studies", J. Am. Chem. Soc.,
|
|
116, 4363-4366 (1994) [Alkali Metal Ions]
|
|
|
|
J. Aqvist, "Ion-Water Interaction Potentials Derived from Free Energy
|
|
Perturbation Simulations", J. Phys. Chem., 94, 8021-8024 (1990)
|
|
[Alkaline Earth Ions, radii adapted for AMBER combining rule]
|
|
|
|
|
|
#############################
|
|
## ##
|
|
## Atom Type Definitions ##
|
|
## ##
|
|
#############################
|
|
|
|
|
|
atom 41 41 OT "TIP3P Water Oxygen" 8 15.999 2
|
|
atom 42 42 HT "TIP3P Hydrogen" 1 1.008 1
|
|
atom 43 43 Li+ "Li+ Lithium Ion" 3 6.941 0
|
|
atom 44 44 Na+ "Na+ Sodium Ion" 11 22.990 0
|
|
atom 45 45 K+ "K+ Potassium Ion" 19 39.098 0
|
|
atom 46 46 Rb+ "Rb+ Rubidium Ion" 37 85.468 0
|
|
atom 47 47 Cs+ "Cs+ Cesium Ion" 55 132.905 0
|
|
atom 48 48 Mg+ "Mg+2 Magnesium Ion" 12 24.305 0
|
|
atom 49 49 Ca+ "Ca+2 Calcium Ion" 20 40.078 0
|
|
atom 50 50 Sr+ "Sr+2 Strontium Ion" 38 87.620 0
|
|
atom 51 51 Ba+ "Ba+2 Barium Ion" 56 137.327 0
|
|
|
|
|
|
################################
|
|
## ##
|
|
## Van der Waals Parameters ##
|
|
## ##
|
|
################################
|
|
|
|
|
|
vdw 41 1.7682 0.1521
|
|
vdw 42 0.2245 0.0460
|
|
vdw 43 1.1371 0.018279
|
|
vdw 44 1.8678 0.002772
|
|
vdw 45 2.6576 0.000328
|
|
vdw 46 2.9558 0.000171
|
|
vdw 47 3.3951 0.000081
|
|
vdw 48 0.7867 0.875044
|
|
vdw 49 1.3260 0.449657
|
|
vdw 50 1.7412 0.118226
|
|
vdw 51 2.1241 0.047096
|
|
|
|
|
|
##################################
|
|
## ##
|
|
## Bond Stretching Parameters ##
|
|
## ##
|
|
##################################
|
|
|
|
|
|
bond 41 42 450.0 0.9572
|
|
|
|
|
|
################################
|
|
## ##
|
|
## Angle Bending Parameters ##
|
|
## ##
|
|
################################
|
|
|
|
|
|
angle 42 41 42 34.05 104.52
|
|
|
|
|
|
###############################
|
|
## ##
|
|
## Urey-Bradley Parameters ##
|
|
## ##
|
|
###############################
|
|
|
|
|
|
ureybrad 42 41 42 38.25 1.5139
|
|
|
|
|
|
########################################
|
|
## ##
|
|
## Atomic Partial Charge Parameters ##
|
|
## ##
|
|
########################################
|
|
|
|
|
|
charge 41 -0.834
|
|
charge 42 0.417
|
|
charge 43 1.000
|
|
charge 44 1.000
|
|
charge 45 1.000
|
|
charge 46 1.000
|
|
charge 47 1.000
|
|
charge 38 2.000
|
|
charge 49 2.000
|
|
charge 50 2.000
|
|
charge 51 2.000
|
|
|
|
|
|
|
|
|