AMBER Archive (2008)

Subject: AMBER: Azobenzene: AMBER+Gromos Force Field parameters

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Wed May 07 2008 - 16:43:17 CDT

Hi
I am modeling Azobenzene with all atoms method.
The following paper shows the complete force field BONDED parameters for the azobenzene compound with GROMACS packages.
I am using their force field parameters in my simulation and trying to reproduce their results which are shown on Fig 2 and Fig 3 in the paper.
IMPROPER and NONBONDED force field parameters are not modified in my simulation simply using AMBER DEFAULT values.
My simulation is in gas phase 300K, so I think non-bonded parameters are not quite important.

Unfortunately, I could NOT get the same results as they did.
Are AMBER and GROMOS force field parameters compatible???
Or, I have made some mistakes???
My .frcmod file and my .prmtop file are shown as follows.

Thanks
Lin

trans-azobenzene--their results
CNNC (180 +-15 degree)
CCNN ( 0 +- 30 degree)

trans-azobenzene--my results
CNNC (180 +-15 degree)
CCNN (the two phenyl rings can rotate freely ; most of time vibrate 0 +- 30 degrees or 120+-30 degrees)

cis-azobenzene--their results
CNNC (-10 +- 20 degree)
CCNN ( -52 +- 17 degree)

cis-azobenzene--my results
CNNC ( 0+- 20 degree)
CCNN ( the two phenyl rings can rotate freely ; most of time vibrate -60+- 30 degrees or 120+-30 degrees)

http://pubs.acs.org/cgi-bin/abstract.cgi/jctcce/2007/3/i05/abs/ct7000733.html
J. Chem. Theory Comput., 3 (5), 1789 -1802, 2007. 10.1021/ct7000733
Atomistic Force Field for Azobenzene Compounds Adapted for QM/MM Simulations with Applications to Liquids and Liquid Crystals

TABLE 2. Nonstandard Force Field Parameters Derived for Azobenzene
                                     force constant trans cis
bonds: NN 1.40*10^3 kJ/mol 1.270 Angstrons 1.255 Angstrons
                               CN 0.72*10^3kJ/mol 1.425 Angstrons 1.440 Angstrons
angles: CNN 650.0 kJ/mol 114 degrees 119 degrees
                               CCN 560.0 kJ/mol 120 degrees 120 degrees
dihedrals: CNNC 70.0 kJ/mol 180 degrees 180 degrees
                               CCNN 6.0 kJ/mol 180 degrees 180 degrees
                               XCCX 40.0 kJ/mol 180 degrees 180 degrees
point charges: N -0.2e -0.2e
                                    C1 0.2e 0.2e
                                    C2-C6 -0.1e -0.1e
                                    H 0.1e 0.1e
                                 

remark goes here
MASS

BOND
ne-nf 334.61 1.255
ca-ne 172.08 1.440
ca-nf 172.08 1.440
ca-ha 293.98 1.09
ca-ca 258.13 1.39

ANGLE
ca-ne-nf 155.35 119.0
ca-nf-ne 155.35 119.0
ca-ca-ne 133.84 120.0
ca-ca-nf 133.84 120.0
ca-ca-ca 133.84 120.0
ca-ca-ha 120.67 120.0

DIHE
ca-ne-nf-ca 2 33.46 180 2.0
ca-nf-ne-ca 2 33.46 180 2.0
ca-ca-ne-nf 2 2.87 180 2.0
ca-ca-nf-ne 2 2.87 180 2.0
ne-nf-ca-ca 2 2.87 180 2.0
nf-ne-ca-ca 2 2.87 180 2.0
ca-ca-ca-ca 2 19.12 180 2.0
ha-ca-ca-ha 2 19.12 180 2.0
ca-ca-ca-ha 2 19.12 180 2.0
ha-ca-ca-ca 2 19.12 180 2.0
ha-ca-ca-ne 2 19.12 180 2.0
ne-ca-ca-ha 2 19.12 180 2.0
ha-ca-ca-nf 2 19.12 180 2.0
nf-ca-ca-ha 2 19.12 180 2.0
ca-ca-ca-ne 2 19.12 180 2.0
ne-ca-ca-ca 2 19.12 180 2.0
ca-ca-ca-nf 2 19.12 180 2.0
nf-ca-ca-ca 2 19.12 180 2.0

IMPROPER
ca-ca-ca-ha 1.1 180.0 2.0 General improper torsional angle (2 general atom types)
ca-ca-ca-ne 1.1 180.0 2.0 Using default value
ca-ca-ca-nf 1.1 180.0 2.0 Using default value

RDPARM MENU: atom
Mask [] represents 24 atoms
Number: Atom Charge Mass ( Residue ) Type Tree
     1: C3 -0.10000 12.0 ( 1:MOL ) ca M
     2: H3 0.10000 1.0 ( 1:MOL ) ha E
     3: C2 -0.10000 12.0 ( 1:MOL ) ca B
     4: H2 0.10000 1.0 ( 1:MOL ) ha E
     5: C1 -0.10000 12.0 ( 1:MOL ) ca B
     6: H1 0.10000 1.0 ( 1:MOL ) ha E
     7: C6 -0.10000 12.0 ( 1:MOL ) ca B
     8: H5 0.10000 1.0 ( 1:MOL ) ha E
     9: C5 -0.10000 12.0 ( 1:MOL ) ca S
    10: H4 0.10000 1.0 ( 1:MOL ) ha E
    11: C4 0.20000 12.0 ( 1:MOL ) ca M
    12: N1 -0.20000 14.0 ( 1:MOL ) ne M
    13: N2 -0.20000 14.0 ( 1:MOL ) nf M
    14: C7 0.20000 12.0 ( 1:MOL ) ca M
    15: C8 -0.10000 12.0 ( 1:MOL ) ca B
    16: H6 0.10000 1.0 ( 1:MOL ) ha E
    17: C9 -0.10000 12.0 ( 1:MOL ) ca B
    18: H7 0.10000 1.0 ( 1:MOL ) ha E
    19: C10 -0.10000 12.0 ( 1:MOL ) ca B
    20: H8 0.10000 1.0 ( 1:MOL ) ha E
    21: C11 -0.10000 12.0 ( 1:MOL ) ca S
    22: H9 0.10000 1.0 ( 1:MOL ) ha E
    23: C12 -0.10000 12.0 ( 1:MOL ) ca M
    24: H10 0.10000 1.0 ( 1:MOL ) ha E

RDPARM MENU: angles
Mask [] represents 24 atoms

  Angle Kthet degrees atom names (numbers)
      1: 120.670 120.00 :1_at_C3 :1_at_C2 :1_at_H2 (1,3,4)
      2: 120.670 120.00 :1_at_H3 :1_at_C3 :1_at_C2 (2,1,3)
      3: 120.670 120.00 :1_at_H3 :1_at_C3 :1_at_C4 (2,1,11)
      4: 120.670 120.00 :1_at_C2 :1_at_C1 :1_at_H1 (3,5,6)
      5: 120.670 120.00 :1_at_H2 :1_at_C2 :1_at_C1 (4,3,5)
      6: 120.670 120.00 :1_at_C1 :1_at_C6 :1_at_H5 (5,7,8)
      7: 120.670 120.00 :1_at_H1 :1_at_C1 :1_at_C6 (6,5,7)
      8: 120.670 120.00 :1_at_C6 :1_at_C5 :1_at_H4 (7,9,10)
      9: 120.670 120.00 :1_at_H5 :1_at_C6 :1_at_C5 (8,7,9)
     10: 120.670 120.00 :1_at_H4 :1_at_C5 :1_at_C4 (10,9,11)
     11: 120.670 120.00 :1_at_C7 :1_at_C8 :1_at_H6 (14,15,16)
     12: 120.670 120.00 :1_at_C7 :1_at_C12 :1_at_H10 (14,23,24)
     13: 120.670 120.00 :1_at_C8 :1_at_C9 :1_at_H7 (15,17,18)
     14: 120.670 120.00 :1_at_H6 :1_at_C8 :1_at_C9 (16,15,17)
     15: 120.670 120.00 :1_at_C9 :1_at_C10 :1_at_H8 (17,19,20)
     16: 120.670 120.00 :1_at_H7 :1_at_C9 :1_at_C10 (18,17,19)
     17: 120.670 120.00 :1_at_C10 :1_at_C11 :1_at_H9 (19,21,22)
     18: 120.670 120.00 :1_at_H8 :1_at_C10 :1_at_C11 (20,19,21)
     19: 120.670 120.00 :1_at_C11 :1_at_C12 :1_at_H10 (21,23,24)
     20: 120.670 120.00 :1_at_H9 :1_at_C11 :1_at_C12 (22,21,23)

     21: 133.840 120.00 :1_at_C3 :1_at_C2 :1_at_C1 (1,3,5)
     22: 133.840 120.00 :1_at_C3 :1_at_C4 :1_at_C5 (1,11,9)
     23: 133.840 120.00 :1_at_C3 :1_at_C4 :1_at_N1 (1,11,12)
     24: 133.840 120.00 :1_at_C2 :1_at_C3 :1_at_C4 (3,1,11)
     25: 133.840 120.00 :1_at_C2 :1_at_C1 :1_at_C6 (3,5,7)
     26: 133.840 120.00 :1_at_C1 :1_at_C6 :1_at_C5 (5,7,9)
     27: 133.840 120.00 :1_at_C6 :1_at_C5 :1_at_C4 (7,9,11)
     28: 133.840 120.00 :1_at_C5 :1_at_C4 :1_at_N1 (9,11,12)
     29: 155.350 119.00 :1_at_C4 :1_at_N1 :1_at_N2 (11,12,13)
     30: 155.350 119.00 :1_at_N1 :1_at_N2 :1_at_C7 (12,13,14)
     31: 133.840 120.00 :1_at_N2 :1_at_C7 :1_at_C8 (13,14,15)
     32: 133.840 120.00 :1_at_N2 :1_at_C7 :1_at_C12 (13,14,23)
     33: 133.840 120.00 :1_at_C7 :1_at_C8 :1_at_C9 (14,15,17)
     34: 133.840 120.00 :1_at_C7 :1_at_C12 :1_at_C11 (14,23,21)
     35: 133.840 120.00 :1_at_C8 :1_at_C7 :1_at_C12 (15,14,23)
     36: 133.840 120.00 :1_at_C8 :1_at_C9 :1_at_C10 (15,17,19)
     37: 133.840 120.00 :1_at_C9 :1_at_C10 :1_at_C11 (17,19,21)
     38: 133.840 120.00 :1_at_C10 :1_at_C11 :1_at_C12 (19,21,23)

RDPARM MENU: dihedrals
Mask [] represents 24 atoms

Dihedral pk phase pn atoms
       1: 9.560 3.14 2.0 :1_at_C3 :1_at_C2 :1_at_C1 :1_at_H1 (1,3,5,6)
       2: 9.560 3.14 2.0 :1_at_C3 :1_at_C4 :1_at_C5 :1_at_H4 (1,11,9,10)
       3: 9.560 3.14 2.0 :1_at_H3 :1_at_C3 :1_at_C2 :1_at_H2 (2,1,3,4)
       4: 9.560 3.14 2.0 :1_at_H3 :1_at_C3 :1_at_C2 :1_at_C1 (2,1,3,5)
       5: 9.560 3.14 2.0 :1_at_H3 :1_at_C3 :1_at_C4 :1_at_C5 (2,1,11,9)
       6: 9.560 3.14 2.0 :1_at_H3 :1_at_C3 :1_at_C4 :1_at_N1 (2,1,11,12)
       7: 9.560 3.14 2.0 :1_at_C2 :1_at_C1 :1_at_C6 :1_at_H5 (3,5,7,8)
       8: 9.560 3.14 2.0 :1_at_C4 :1_at_C3 :1_at_C2 :1_at_H2 (11,1,3,4)
       9: 9.560 3.14 2.0 :1_at_H2 :1_at_C2 :1_at_C1 :1_at_H1 (4,3,5,6)
      10: 9.560 3.14 2.0 :1_at_H2 :1_at_C2 :1_at_C1 :1_at_C6 (4,3,5,7)
      11: 9.560 3.14 2.0 :1_at_C1 :1_at_C6 :1_at_C5 :1_at_H4 (5,7,9,10)
      12: 9.560 3.14 2.0 :1_at_H1 :1_at_C1 :1_at_C6 :1_at_H5 (6,5,7,8)
      13: 9.560 3.14 2.0 :1_at_H1 :1_at_C1 :1_at_C6 :1_at_C5 (6,5,7,9)
      14: 9.560 3.14 2.0 :1_at_H5 :1_at_C6 :1_at_C5 :1_at_H4 (8,7,9,10)
      15: 9.560 3.14 2.0 :1_at_H5 :1_at_C6 :1_at_C5 :1_at_C4 (8,7,9,11)
      16: 9.560 3.14 2.0 :1_at_H4 :1_at_C5 :1_at_C4 :1_at_N1 (10,9,11,12)
      17: 9.560 3.14 2.0 :1_at_N2 :1_at_C7 :1_at_C8 :1_at_H6 (13,14,15,16)
      18: 9.560 3.14 2.0 :1_at_N2 :1_at_C7 :1_at_C12 :1_at_H10 (13,14,23,24)
      19: 9.560 3.14 2.0 :1_at_C7 :1_at_C8 :1_at_C9 :1_at_H7 (14,15,17,18)
      20: 9.560 3.14 2.0 :1_at_C7 :1_at_C12 :1_at_C11 :1_at_H9 (14,23,21,22)
      21: 9.560 3.14 2.0 :1_at_C8 :1_at_C7 :1_at_C12 :1_at_H10 (15,14,23,24)
      22: 9.560 3.14 2.0 :1_at_C8 :1_at_C9 :1_at_C10 :1_at_H8 (15,17,19,20)
      23: 9.560 3.14 2.0 :1_at_H6 :1_at_C8 :1_at_C7 :1_at_C12 (16,15,14,23)
      24: 9.560 3.14 2.0 :1_at_H6 :1_at_C8 :1_at_C9 :1_at_H7 (16,15,17,18)
      25: 9.560 3.14 2.0 :1_at_H6 :1_at_C8 :1_at_C9 :1_at_C10 (16,15,17,19)
      26: 9.560 3.14 2.0 :1_at_C9 :1_at_C10 :1_at_C11 :1_at_H9 (17,19,21,22)
      27: 9.560 3.14 2.0 :1_at_H7 :1_at_C9 :1_at_C10 :1_at_H8 (18,17,19,20)
      28: 9.560 3.14 2.0 :1_at_H7 :1_at_C9 :1_at_C10 :1_at_C11 (18,17,19,21)
      29: 9.560 3.14 2.0 :1_at_C10 :1_at_C11 :1_at_C12 :1_at_H10 (19,21,23,24)
      30: 9.560 3.14 2.0 :1_at_H8 :1_at_C10 :1_at_C11 :1_at_H9 (20,19,21,22)
      31: 9.560 3.14 2.0 :1_at_H8 :1_at_C10 :1_at_C11 :1_at_C12 (20,19,21,23)
      32: 9.560 3.14 2.0 :1_at_H9 :1_at_C11 :1_at_C12 :1_at_H10 (22,21,23,24)
B 33: 1.100 3.14 2.0 :1_at_H3 :1_at_C3 :1_at_C4 :1_at_C2 (2,1,11,3)
B 34: 1.100 3.14 2.0 :1_at_C3 :1_at_C1 :1_at_C2 :1_at_H2 (1,5,3,4)
B 35: 1.100 3.14 2.0 :1_at_C2 :1_at_C6 :1_at_C1 :1_at_H1 (3,7,5,6)
B 36: 1.100 3.14 2.0 :1_at_C1 :1_at_C5 :1_at_C6 :1_at_H5 (5,9,7,8)
B 37: 1.100 3.14 2.0 :1_at_C6 :1_at_C4 :1_at_C5 :1_at_H4 (7,11,9,10)
B 38: 1.100 3.14 2.0 :1_at_C7 :1_at_C9 :1_at_C8 :1_at_H6 (14,17,15,16)
B 39: 1.100 3.14 2.0 :1_at_C8 :1_at_C10 :1_at_C9 :1_at_H7 (15,19,17,18)
B 40: 1.100 3.14 2.0 :1_at_C9 :1_at_C11 :1_at_C10 :1_at_H8 (17,21,19,20)
B 41: 1.100 3.14 2.0 :1_at_C10 :1_at_C12 :1_at_C11 :1_at_H9 (19,23,21,22)
B 42: 1.100 3.14 2.0 :1_at_C7 :1_at_C11 :1_at_C12 :1_at_H10 (14,21,23,24)

      43: 9.560 3.14 2.0 :1_at_C3 :1_at_C2 :1_at_C1 :1_at_C6 (1,3,5,7)
E 44: 9.560 3.14 2.0 :1_at_C3 :1_at_C4 :1_at_C5 :1_at_C6 (1,11,9,7)
      45: 1.435 3.14 2.0 :1_at_C3 :1_at_C4 :1_at_N1 :1_at_N2 (1,11,12,13)
      46: 9.560 3.14 2.0 :1_at_C2 :1_at_C3 :1_at_C4 :1_at_C5 (3,1,11,9)
      47: 9.560 3.14 2.0 :1_at_C2 :1_at_C3 :1_at_C4 :1_at_N1 (3,1,11,12)
E 48: 9.560 3.14 2.0 :1_at_C2 :1_at_C1 :1_at_C6 :1_at_C5 (3,5,7,9)
      49: 9.560 3.14 2.0 :1_at_C4 :1_at_C3 :1_at_C2 :1_at_C1 (11,1,3,5)
E 50: 9.560 3.14 2.0 :1_at_C1 :1_at_C6 :1_at_C5 :1_at_C4 (5,7,9,11)
      51: 9.560 3.14 2.0 :1_at_C6 :1_at_C5 :1_at_C4 :1_at_N1 (7,9,11,12)
      52: 1.435 3.14 2.0 :1_at_C5 :1_at_C4 :1_at_N1 :1_at_N2 (9,11,12,13)
      53: 16.730 3.14 2.0 :1_at_C4 :1_at_N1 :1_at_N2 :1_at_C7 (11,12,13,14)
      54: 1.435 3.14 2.0 :1_at_N1 :1_at_N2 :1_at_C7 :1_at_C8 (12,13,14,15)
      55: 1.435 3.14 2.0 :1_at_N1 :1_at_N2 :1_at_C7 :1_at_C12 (12,13,14,23)
      56: 9.560 3.14 2.0 :1_at_N2 :1_at_C7 :1_at_C8 :1_at_C9 (13,14,15,17)
      57: 9.560 3.14 2.0 :1_at_N2 :1_at_C7 :1_at_C12 :1_at_C11 (13,14,23,21)
      58: 9.560 3.14 2.0 :1_at_C7 :1_at_C8 :1_at_C9 :1_at_C10 (14,15,17,19)
E 59: 9.560 3.14 2.0 :1_at_C7 :1_at_C12 :1_at_C11 :1_at_C10 (14,23,21,19)
      60: 9.560 3.14 2.0 :1_at_C8 :1_at_C7 :1_at_C12 :1_at_C11 (15,14,23,21)
E 61: 9.560 3.14 2.0 :1_at_C8 :1_at_C9 :1_at_C10 :1_at_C11 (15,17,19,21)
      62: 9.560 3.14 2.0 :1_at_C9 :1_at_C8 :1_at_C7 :1_at_C12 (17,15,14,23)
E 63: 9.560 3.14 2.0 :1_at_C9 :1_at_C10 :1_at_C11 :1_at_C12 (17,19,21,23)
B 64: 1.100 3.14 2.0 :1_at_C3 :1_at_C5 :1_at_C4 :1_at_N1 (1,9,11,12)
B 65: 1.100 3.14 2.0 :1_at_C8 :1_at_C12 :1_at_C7 :1_at_N2 (15,23,14,13)

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