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
