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 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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