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 <[email protected]> > 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 [email protected] > > 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 [email protected]. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
