[gmx-users] gold-protein simulation

[Justin Lemkul]

On 1/5/13 2:54 PM, fatemeh ramezani wrote:
>
>
>   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.
>

An interaction that is defined in ffbonded.itp simply means that mdrun knows how 
to incorporate that term into the energy of the system if it is present.  Bonds 
do not break and form in MD simulations, so the presence of this bond in 
ffbonded.itp does nothing unless the bond is actually present in the topology file.

-Justin

> 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
>

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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