[gmx-users] gold-protein simulation

[fatemeh ramezani]

 HI
I'm simulating gold nanoparticle interaction with protein by oplsaa forcefield . I added AU-AU Lennard Jones parameters to ffnonbonded.itp and also I added what was necessary for AU atom simulation in .atp , .rtp files.
what I see After simulation shows that my simulation is wrong.Despite the Epsilon and Sigma between the gold atom  and  any other atoms still have not entered, but the protein is drawn in, and gold cluster is placed in a specified intervalfrom protein, Which is probably due to hydrophobic forces(Of course this is a guess.). To eliminate this tension forces ,the hydrophobic bonds between gold atoms and protein, what should I do?
This causes, I can not studycovalently interaction between a gold atom and a sulfur atom of cysteine​​,And to add the gold-sulfur bond parameters in the file ffbonded.itpor not, has no effect on the behavior of the system. However, the gold cluster is drawn in toward each type of amino acid (Cys , Ser, Phe,...) that I'm simulating.

Hope, I could say what I mean?

pdb file:
HETATM    1 AU1  AU      1      -3.475  -3.478  -3.478
HETATM    2 AU2  AU      2      -1.135  -3.460  -1.141
HETATM    3 AU3  AU      3      -1.134  -1.141  -3.459
HETATM    4 AU4  AU      4      -3.465  -1.144  -1.144
HETATM    5 AU1  AU      5      -3.482  -3.483   1.159
HETATM    6 AU2  AU      6      -1.145  -3.473   3.485
HETATM    7 AU3  AU      7      -1.132  -1.134   1.147
HETATM    8 AU4  AU      8      -3.482  -1.155   3.486
HETATM    9 AU1  AU      9      -3.481   1.160  -3.484
HETATM   10 AU2  AU     10      -1.130   1.150  -1.136
HETATM   11 AU3  AU     11      -1.136   3.487  -3.463
HETATM   12 AU4  AU     12      -3.484   3.486  -1.156
HETATM   13 AU1  AU     13      -3.468   1.146   1.146
HETATM   14 AU2  AU     14      -1.128   1.152   3.462
HETATM   15 AU3  AU     15      -1.136   3.464   1.147
HETATM   16 AU4  AU     16      -3.478   3.479   3.479
HETATM   17 AU1  AU     17       1.172  -3.476  -3.475
HETATM   18 AU2  AU     18       3.510  -3.458  -1.135
HETATM   19 AU3  AU     19       3.508  -1.139  -3.464
HETATM   20 AU4  AU     20       1.189  -1.124  -1.122
HETATM   21 AU1  AU     21       1.173  -3.443   1.151
HETATM   22 AU2  AU     22       3.517  -3.447   3.466
HETATM   23 AU3  AU     23       3.605  -1.093   1.172
HETATM   24 AU4  AU     24       1.189  -1.120   3.454
HETATM   25 AU1  AU     25       1.173   1.152  -3.441
HETATM   26 AU2  AU     26       3.613   1.157  -1.098
HETATM   27 AU3  AU     27       3.515   3.468  -3.451
HETATM   28 AU4  AU     28       1.225   3.459  -1.089
HETATM   29 AU1  AU     29       1.222   1.160   1.149
HETATM   30 AU2  AU     30       3.590   1.202   3.496
HETATM   31 AU3  AU     31       3.885   3.421   1.223
HETATM   32 AU4  AU     32       1.225   3.488   3.443
ATOM     33  N   CYS     1      24.186  -2.798  -5.621
ATOM     34  CA  CYS     1      23.683  -2.334  -4.353
ATOM     35  C   CYS     1      22.286  -2.877  -4.134
ATOM     36  O   CYS     1      22.042  -3.954  -3.643
ATOM     37  CB  CYS     1      23.711  -0.798  -4.335
ATOM     38  SG  CYS     1      23.112  -0.148  -2.772
CONECT   33   34
CONECT   34   33   35   37
CONECT   35   34   36
CONECT   36   35
CONECT   37   34   38
CONECT   38   37
CONECT    0   33
CONECT    0   34
CONECT    0   37
CONECT    0   37
CONECT    0   38
CONECT    0   38
CONECT    0   38
END




Fatemeh Ramezani