Re: [gmx-users] gold-S simulation
On 12/19/12 6:02 AM, fatemeh ramezani wrote: Dear Justin I want exactly this, that the distance between Au-S be stable around equilibrium value, For this purpose,Should I put the harmonic parameters related to the gold and sulfur in ffbonded file? Or I should consider AU-S connection as VonderWaals and put its epsilon and sidma in ffnonbonded file? Please be mindful to only parse the relevant portion of the digest and to use a real subject line. Yes, if you want there to be a covalent bond, you need to introduce one. Hoping that van der Waals parameters will hold the elements of the system in place does not sound like a robust approach to me. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
Re: [gmx-users] gold-S simulation
Dear francesco I extract gold parameter from papers that I attached them for you. But for gold and other atom parameters, you should calculate them using common combination rule. Fatemeh Ramezani -- gmx-users mailing listgmx-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
Re: [gmx-users] gold-S simulation
hi thanks for your attention, all itp files are in OPLSAA forcefield folder that I attached it for you. Fatemeh Ramezani -- gmx-users mailing listgmx-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
Re: [gmx-users] gold-S simulation
Hi fatemeh, thank you for the references. Regarding your problem, what does it means you don't see any interaction? Is it possible it is just a problem of the visualization software. To be sure, you could monitor the distance between any S atom and the Au atom to which it is supposed to be bound. If the distance is stable around the equilibrium value you can say that the interaction is still present Francesco 2012/12/16 fatemeh ramezani fr_...@yahoo.com hi thanks for your attention, all itp files are in OPLSAA forcefield folder that I attached it for you. Fatemeh Ramezani -- gmx-users mailing listgmx-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 -- Cordiali saluti, Dr.Oteri Francesco -- gmx-users mailing listgmx-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
Re: [gmx-users] gold-S simulation
On 12/16/12 1:11 PM, francesco oteri wrote: Hi fatemeh, thank you for the references. Regarding your problem, what does it means you don't see any interaction? Is it possible it is just a problem of the visualization software. To be sure, you could monitor the distance between any S atom and the Au atom to which it is supposed to be bound. If the distance is stable around the equilibrium value you can say that the interaction is still present In addition, if one is expecting some sort of covalent association, it must be defined in the topology. This will not be true in the case of protein-Au interactions unless one makes appropriate entries in specbond.dat, similar to heme, or manual addition. Bonded parameters are useless unless there is a bond :) -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
Re: [gmx-users] gold-S simulation
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 0.0e+00 0.0e+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 3.2e-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 listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
Re: [gmx-users] gold-S simulation
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 p...@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: HETATM1 N CYS 1 0.000 1.335 0.000 HETATM2 CA CYS 1 -0.683 1.818 -1.183 HETATM3 C CYS 1 -0.705 3.339 -1.221 HETATM4 O CYS 1 -0.184 3.993 -0.319 HETATM5 CB CYS 1 -2.127 1.330 -1.221 HETATM6 SG CYS 1 -3.106 1.859 -2.649 HETATM8 AU AU 8 -2.833 0.428 -1.793 HETATM9 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 CONECT12 CONECT01 CONECT2135 CONECT02 CONECT324 CONECT43 CONECT526 CONECT05 CONECT05 CONECT65 CONECT06 CONECT06 CONECT06 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 1428.08000 0.000A3.38550e-01 2.44704e+00 AU AU 79 196.9700 0.000 A0.29510e+00 22.1120e+00 [ nonbond_params ] AU AU 10.0e+00 0.0e+00 ; SC 08/2007: Special Au-N vdw to simulate chemical bond between gold-imidazole AU opls_511 13.07000e-01 3.96000e+00 ; SC 05/2008: special Au-C and Au-H to simulate pi-systems alkenes+benzene (and PHE) AU opls_142 13.21000e-1 2.65400e+00 AU opls_143 13.21000e-1 2.65400e+00 AU opls_144 12.67000e-1 1.66500e+00 AU opls_145 13.2e-1 2.54600e+00 AU opls_146 12.67000e-1 1.66500e+00 AU opls_150 13.21000e-1 2.65400e+00 ; +imidazole and His AU opls_506 13.21000e-1 2.54000e+00 AU opls_507 13.21000e-1 2.54000e+00 AU opls_508 13.21000e-1 2.54000e+00 ; +HisH AU opls_509 13.21000e-1 2.54000e+00 AU opls_510 13.21000e-1 2.54000e+00 ; +TYR AU opls_166 13.21000e-1 2.54000e+00 ; +TRP AU opls_500 13.21000e-1 2.54000e+00 AU opls_514 13.21000e-1 2.54000e+00 AU opls_501 13.21000e-1 2.54000e+00 AU opls_502 13.55000e-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 ] ; ij func b0 kb . . . AUSH 10.24000 165528.0 ; AUS 10.24000 165528.0 ; AUSG 10.24000 165528.0 ; . . . [ angletypes ] ; ijk 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_C19 0.9196 2 #define improper_AU_SG_C_C19 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
