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
--
========================================
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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