[gmx-users] gold-S simulation

[fatemeh ramezani]

hi 


I'm simulating gold atom interaction with  aminoacidcys. I have made gold-cys.pdb by hyperchem software:

HETATM    1  N   CYS     1       0.000   1.335   0.000
HETATM    2  CA  CYS     1      -0.683   1.818  -1.183
HETATM    3  C   CYS     1      -0.705   3.339  -1.221
HETATM    4  O   CYS     1      -0.184   3.993  -0.319
HETATM    5  CB  CYS     1      -2.127   1.330  -1.221
HETATM    6  SG  CYS     1      -3.106   1.859  -2.649
HETATM    8 AU   AU      8      -2.833   0.428  -1.793
HETATM    9 AU   AU      9      -2.647   0.381  -2.869
HETATM   10 AU   AU     10      -1.691   1.360  -3.093
HETATM   11 AU   AU     11      -0.647   2.706  -2.135
HETATM   12 AU   AU     12      -2.742   0.834  -0.456
HETATM   13 AU   AU     13      -1.691   2.061  -0.043
HETATM   14 AU   AU     14      -0.783   3.136   0.376
HETATM   15 AU   AU     15       0.095   3.750  -1.068
HETATM   16 AU   AU     16      -2.929   2.480  -2.204
HETATM   17 AU   AU     17      -3.285   1.594  -3.328
HETATM   18 AU   AU     18      -2.544   2.593  -3.763
HETATM   19 AU   AU     19      -1.951   1.260  -2.303
CONECT    1    2
CONECT    0    1
CONECT    2    1    3    5
CONECT    0    2
CONECT    3    2    4
CONECT    4    3
CONECT    5    2    6
CONECT    0    5
CONECT    0    5
CONECT    6    5
CONECT    0    6
CONECT    0    6
CONECT    0    6
END

 

I started simulation by this pdb file. I'm using OPLSAA force field and also I added gold parameter in ffnonbonded.itp  :
.
.
.
; Added by DvdS 05/2005 copied from GROMACS force field.       
 SI         SI     14    28.08000     0.000        A    3.38550e-01  2.44704e+00
 AU         AU     79   196.9700     0.000       A    0.29510e+00  22.1120e+00

[ nonbond_params ]
AU          AU                                   1    0.00000e+00  0.00000e+00


; SC 08/2007: Special Au-N vdw to simulate chemical bond between gold-imidazole
 AU         opls_511                             1    3.07000e-01  3.96000e+00
 
; SC 05/2008: special Au-C and Au-H to simulate pi-systems alkenes+benzene (and PHE)
 AU         opls_142                             1    3.21000e-1   2.65400e+00
 AU         opls_143                             1    3.21000e-1   2.65400e+00
 AU         opls_144                             1    2.67000e-1   1.66500e+00
 AU         opls_145                             1    3.20000e-1   2.54600e+00
 AU         opls_146                             1    2.67000e-1   1.66500e+00
 AU         opls_150                             1    3.21000e-1   2.65400e+00
 
; +imidazole and His
 AU         opls_506                             1    3.21000e-1   2.54000e+00
 AU         opls_507                             1    3.21000e-1   2.54000e+00
 AU         opls_508                             1    3.21000e-1   2.54000e+00

; +HisH
 AU         opls_509                             1    3.21000e-1   2.54000e+00
 AU         opls_510                             1    3.21000e-1   2.54000e+00
; +TYR
 AU         opls_166                             1    3.21000e-1   2.54000e+00
; +TRP
 AU         opls_500                             1    3.21000e-1   2.54000e+00
 AU         opls_514                             1    3.21000e-1   2.54000e+00
 AU         opls_501                             1    3.21000e-1   2.54000e+00
 AU         opls_502                             1    3.55000e-1   3.55000e+00

and I concidered AU-S as bonding connection and I added its parameter (bond stretch, dihedral and angle ) in ffbonded.itp file: 
[ bondtypes ]
; i    j  func       b0          kb
.
.
.
AU    SH      1    0.24000   165528.0   ;
AU    S       1    0.24000   165528.0   ;
AU    SG      1    0.24000   165528.0   ;
.
.
.
[ angletypes ]
;  i    j    k  func       th0       cth
.
.
.
  AU     SG     CB      1   109.00     46.34
  AU     SH     CB      1   109.00     46.34
  AU     S      CB      1   109.00     46.34
.
.
.
[ dihedraltypes ]
.
.
.
#define improper_AU_S_CB_CA    -180.0      1.2958     2 

#define improper_AU_SH_CB_CA   -180.0      1.2958     2

#define improper_AU_SG_CB_CA    -180       1.2958     2

#define improper_AU_S_C_C         19       0.9196     2

#define improper_AU_SH_C_C        19       0.9196     2

#define improper_AU_SG_C_C        19       0.9196     2
.
.
.

when I run my simulation I dont see any interaction or affinity between gold atom and S atom of cystein, while it is clear that gold shoud has interaction with sulfur. what is its reason? I'm completely confused. I tried anythings that I can but my system doesn't work.

please help me
 

Fatemeh Ramezani