[gmx-users] gold-S simulation
francesco oteri
francesco.oteri at gmail.com
Sun Dec 16 04:34:20 CET 2012
Hi fatemeh,
I am looking for prameters like yours, where have you took the parameters
for gold and gold-aminoacid inteaction?
Francesco
2012/12/16 Peter C. Lai <pcl at uab.edu>
> 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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--
Cordiali saluti, Dr.Oteri Francesco
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