[gmx-users] gold-S simulation
Peter C. Lai
pcl at uab.edu
Sun Dec 16 04:13:15 CET 2012
Where is the .itp file for the system?
On 2012-12-15 01:40:27PM -0800, fatemeh ramezani wrote:
> 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
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