From owner-chemistry@ccl.net Sat Sep 8 06:31:01 2007 From: "Daniel Jana dfjana_._gmail.com" To: CCL Subject: CCL: g03: hypervalent warning!!?? Message-Id: <-35106-070908062023-22767-K7+Wqw5IaQWIEMvqqgcs8Q===server.ccl.net> X-Original-From: Daniel Jana Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sat, 08 Sep 2007 10:17:38 +0100 MIME-Version: 1.0 Sent to CCL by: Daniel Jana [dfjana(!)gmail.com] Kaci Tizi_Ouzou kaci.tiziouzou##gmail.com wrote: > Warning: Cl atom 2 may be hypervalent but has no d functions > > Does anybody know what this message is all about (and if there is a > known solution) to make geometry optimization complete. Hello! If I am not mistaken, the reason you have this message is due to the choice of basis set, which has no d functions, like 3-21G or 6-31G. You should add some d functions 6-31G**, for instance and that message will go away. Cheers, Daniel From owner-chemistry@ccl.net Sat Sep 8 12:48:01 2007 From: "Kalyan chaitanya kalyanpulipaka^-^gmail.com" To: CCL Subject: CCL: query reagrding docking through Molecular Dynamics Message-Id: <-35107-070908123939-16659-OKi/gbJOmUpIL7Hhac9T7A**server.ccl.net> X-Original-From: "Kalyan chaitanya" Content-Type: multipart/alternative; boundary="----=_Part_6257_14973835.1189269562271" Date: Sat, 8 Sep 2007 22:09:22 +0530 MIME-Version: 1.0 Sent to CCL by: "Kalyan chaitanya" [kalyanpulipaka===gmail.com] ------=_Part_6257_14973835.1189269562271 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear all, Presently am working on Molecular docking, both protein-ligand and protein-protein docking now iam intrested in tlooking at conformational changes of receptor while docking, which is possible to through Molecular Dynamics (as per my knowledge), but i don't know as to what softwares are available for the same purpose and also please let me know if any one has any tutorrial for the same. Thank you in advance, Regards, Kalyan. ------=_Part_6257_14973835.1189269562271 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline

Dear all,

Presently am working on Molecular docking, both protein-ligand and protein-protein docking now iam intrested in tlooking at conformational changes of receptor while docking, which is possible to through Molecular Dynamics (as per my knowledge), but i don't know as to what softwares are available for the same purpose and also please let me know if any one has any tutorrial for the same.

Thank you in advance,

Regards,

Kalyan.

------=_Part_6257_14973835.1189269562271-- From owner-chemistry@ccl.net Sat Sep 8 13:25:00 2007 From: "hadi behzadi hadi.behzadi**gmail.com" To: CCL Subject: CCL: scan Message-Id: <-35108-070908121341-14602-eFlu6LBm7LPdrndBuUhQ5w-$-server.ccl.net> X-Original-From: "hadi behzadi" Date: Sat, 8 Sep 2007 12:13:37 -0400 Sent to CCL by: "hadi behzadi" [hadi.behzadi*_*gmail.com] Dear all, I am trying to do a PES scan for Fe-O distance between 1.75-8 A in heme with one and two water as a axial ligand. I have two problem in this relation as follow: 1- For heme with one water the calculation give me error in 4.1 A because of failure to convergence, the energy profile is good befor this distance.I use SCF(maxcycle=5000) and the B3lyp method with the follow basis sets: n,o 6-31g* c,h sto-3g fe lanl2dz 2- For heme with two water as a axial ligand,one water is fixed, the energy profile is not good due to the break in energy profile in 2.35 and 2.45 A. Here is the obtained energy and used basis sets: n,o,c,h 3-21g* fe lanl2dz Distance Energy(A.U) 1.75 -2392.47636390 1.85 -2392.48624467 1.95 -2392.48987980 2.05 -2392.49028130 2.15 -2392.48885147 2.25 -2392.48631707 2.35 -2392.48316683 2.45 -2392.58475917 2.55 -2392.58231643 2.65 -2392.57967485 2.75 -2392.57698884 2.85 -2392.57434438 2.95 -2392.57179832 3.05 -2392.56938208 3.15 -2392.56710231 I really don t underestand what is the problem and any Help would be appreciated. Regards