From owner-chemistry@ccl.net Sat Jan 5 04:31:00 2013 From: "Elham Abdolhamidi flight.66.ab[-]gmail.com" To: CCL Subject: CCL:G: finding energy levels of polymers using Gaussian Message-Id: <-48043-130105042929-14277-ETc9kVj+VqHwexQEb/3djg[-]server.ccl.net> X-Original-From: "Elham Abdolhamidi" Date: Sat, 5 Jan 2013 04:29:28 -0500 Sent to CCL by: "Elham Abdolhamidi" [flight.66.ab]![gmail.com] Dear Members; I'm using Gaussian09 to find energy levels of polymers. When I activate PBC (in GaussView), the Solvation button becomes deactivated. I do not know the reason, and how I can apply the solvent effect. I'll be thankful if you help me finding the answer. Elham From owner-chemistry@ccl.net Sat Jan 5 18:48:00 2013 From: "fatemeh ramezani fr_750%a%yahoo.com" To: CCL Subject: CCL: gold-protein simulation Message-Id: <-48044-130105151237-28065-Jv0Xy7jhrL+fIaletiFl3w^server.ccl.net> X-Original-From: "fatemeh ramezani" Date: Sat, 5 Jan 2013 15:12:36 -0500 Sent to CCL by: "fatemeh ramezani" [fr_750 _ yahoo.com] HI I'm simulating gold nanoparticle interaction with protein by oplsaa forcefield . I added AU-AU Lennard Jones parameters to ffnonbonded.itp and also I added what was necessary for AU atom simulation in .atp , .rtp files. what I see After simulation shows that my simulation is wrong. Despite the Epsilon and Sigma between the gold atom and any other atoms still have not entered, but the protein is drawn in, and gold cluster is placed in a specified interval from protein, Which is probably due to hydrophobic forces(Of course this is a guess.). To eliminate this tension forces ,the hydrophobic bonds between gold atoms and protein, what should I do? This causes, I can not study covalently interaction between a gold atom and a sulfur atom of cysteine??, And to add the gold-sulfur bond parameters in the file ffbonded.itp or not, has no effect on the behavior of the system. However, the gold cluster is drawn in toward each type of amino acid (Cys , Ser, Phe,...) that I'm simulating. Hope, I could say what I mean? pdb file: HETATM 1 AU1 AU 1 -3.475 -3.478 -3.478 HETATM 2 AU2 AU 2 -1.135 -3.460 -1.141 HETATM 3 AU3 AU 3 -1.134 -1.141 -3.459 HETATM 4 AU4 AU 4 -3.465 -1.144 -1.144 HETATM 5 AU1 AU 5 -3.482 -3.483 1.159 HETATM 6 AU2 AU 6 -1.145 -3.473 3.485 HETATM 7 AU3 AU 7 -1.132 -1.134 1.147 HETATM 8 AU4 AU 8 -3.482 -1.155 3.486 HETATM 9 AU1 AU 9 -3.481 1.160 -3.484 HETATM 10 AU2 AU 10 -1.130 1.150 -1.136 HETATM 11 AU3 AU 11 -1.136 3.487 -3.463 HETATM 12 AU4 AU 12 -3.484 3.486 -1.156 HETATM 13 AU1 AU 13 -3.468 1.146 1.146 HETATM 14 AU2 AU 14 -1.128 1.152 3.462 HETATM 15 AU3 AU 15 -1.136 3.464 1.147 HETATM 16 AU4 AU 16 -3.478 3.479 3.479 HETATM 17 AU1 AU 17 1.172 -3.476 -3.475 HETATM 18 AU2 AU 18 3.510 -3.458 -1.135 HETATM 19 AU3 AU 19 3.508 -1.139 -3.464 HETATM 20 AU4 AU 20 1.189 -1.124 -1.122 HETATM 21 AU1 AU 21 1.173 -3.443 1.151 HETATM 22 AU2 AU 22 3.517 -3.447 3.466 HETATM 23 AU3 AU 23 3.605 -1.093 1.172 HETATM 24 AU4 AU 24 1.189 -1.120 3.454 HETATM 25 AU1 AU 25 1.173 1.152 -3.441 HETATM 26 AU2 AU 26 3.613 1.157 -1.098 HETATM 27 AU3 AU 27 3.515 3.468 -3.451 HETATM 28 AU4 AU 28 1.225 3.459 -1.089 HETATM 29 AU1 AU 29 1.222 1.160 1.149 HETATM 30 AU2 AU 30 3.590 1.202 3.496 HETATM 31 AU3 AU 31 3.885 3.421 1.223 HETATM 32 AU4 AU 32 1.225 3.488 3.443 ATOM 33 N CYS 1 24.186 -2.798 -5.621 ATOM 34 CA CYS 1 23.683 -2.334 -4.353 ATOM 35 C CYS 1 22.286 -2.877 -4.134 ATOM 36 O CYS 1 22.042 -3.954 -3.643 ATOM 37 CB CYS 1 23.711 -0.798 -4.335 ATOM 38 SG CYS 1 23.112 -0.148 -2.772 CONECT 33 34 CONECT 34 33 35 37 CONECT 35 34 36 CONECT 36 35 CONECT 37 34 38 CONECT 38 37 CONECT 0 33 CONECT 0 34 CONECT 0 37 CONECT 0 37 CONECT 0 38 CONECT 0 38 CONECT 0 38 END Fatemeh Ramezani