From owner-chemistry@ccl.net Tue Nov 28 10:14:01 2017 From: "Pavel pavel_polishchuk[a]ukr.net" To: CCL Subject: CCL: 3rd advanced in silico drug design workshop in Olomouc Message-Id: <-53076-171128030150-6348-PSTPEK2lD5Kw09N9xYwJtg---server.ccl.net> X-Original-From: Pavel Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Tue, 28 Nov 2017 09:01:43 +0100 MIME-Version: 1.0 Sent to CCL by: Pavel [pavel_polishchuk-#-ukr.net] Dear colleagues, We would like to invite you on the 3rd Drug Design workshop which will be held in Olomouc 23-26 January 2018. It is focused on practical applications of different chemoinformatic tools for drug development. This might be interesting for bachelor, master and PhD students to broaden their experience and sharpen skills   During the workshop, students will learn pharmacophore modeling with LigandScout, molecular docking with AutoDock Vina, QSAR modeling with RDKit and SPCI. A competition will be organized on the final day of the workshop where participants will be able to apply acquired knowledge to real chemoinformatic tasks. http://fch.upol.cz/en/research/conferences-workshops/3add/   Please feel free to share this information to those who can be interested in participation in such event. Thank you. Kind regards, Pavel. -- Dr. Pavel Polishchuk senior researcher Institute of Molecular and Translational Medicine Faculty of Medicine and Dentistry Palacky University Hněvotínská 1333/5 779 00 Olomouc Czech Republic +420 585632298 From owner-chemistry@ccl.net Tue Nov 28 12:28:00 2017 From: "Morad El-Hendawy morad.elhendawy^_^yahoo.com" To: CCL Subject: CCL:G: Gaussian 09W program was freezing during the processing Message-Id: <-53077-171128114910-23539-xSBAqeddbpZMjKFMAsW+tg=-=server.ccl.net> X-Original-From: "Morad El-Hendawy" Date: Tue, 28 Nov 2017 11:49:09 -0500 Sent to CCL by: "Morad El-Hendawy" [morad.elhendawy-,-yahoo.com] Dear CCLers, Recently we bought a server with Intel Xeon Processor E5-2698 v4 then installed Windows Server 2008 (64 bit) operating system. We installed Gaussian 09W program properly and tested methane molecule for single point energy calculation but the program stopped at two electron integral calculations stage. Although PM6 was used for computation but the program was freezing. Herein, you can see the output. Gaussian 09: IA32W-G09RevA.02 11-Jun-2009 27-Nov-2017 ****************************************** ----------------------- # pm6 geom=connectivity ----------------------- 1/38=1,57=2/1; 2/12=2,17=6,18=5,40=1/2; 3/5=2,16=1,25=1,41=3900000/1,2,3; 4/35=1/1; 5/5=2,35=1,38=5/2; 6/7=2,8=2,9=2,10=2,28=1/1; 99/5=1,9=1/99; ------------------- Title Card Required ------------------- Symbolic Z-matrix: Charge = 0 Multiplicity = 1 C 0.46908 0.2234 -0.01464 H 0.82574 -0.78541 -0.01464 H 0.82576 0.7278 0.85901 H 0.82576 0.7278 -0.88829 H -0.60092 0.22341 -0.01464 Input orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 6 0 0.469083 0.223401 -0.014643 2 1 0 0.825738 -0.785409 -0.014643 3 1 0 0.825756 0.727799 0.859009 4 1 0 0.825756 0.727799 -0.888294 5 1 0 -0.600917 0.223414 -0.014643 --------------------------------------------------------------------- Distance matrix (angstroms): 1 2 3 4 5 1 C 0.000000 2 H 1.070000 0.000000 3 H 1.070000 1.747302 0.000000 4 H 1.070000 1.747302 1.747303 0.000000 5 H 1.070000 1.747303 1.747303 1.747303 0.000000 Stoichiometry CH4 Framework group T[O(C),4C3(H)] Deg. of freedom 1 Full point group T NOp 12 Largest Abelian subgroup D2 NOp 4 Largest concise Abelian subgroup D2 NOp 4 Standard orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 6 0 0.000000 0.000000 0.000000 2 1 0 0.617765 0.617765 0.617765 3 1 0 -0.617765 -0.617765 0.617765 4 1 0 -0.617765 0.617765 -0.617765 5 1 0 0.617765 -0.617765 -0.617765 --------------------------------------------------------------------- Rotational constants (GHZ): 164.2463785 164.2463785 164.2463785 Standard basis: VSTO-6G (5D, 7F) There are 2 symmetry adapted basis functions of A symmetry. There are 2 symmetry adapted basis functions of B1 symmetry. There are 2 symmetry adapted basis functions of B2 symmetry. There are 2 symmetry adapted basis functions of B3 symmetry. Integral buffers will be 262144 words long. Regular integral format. Two-electron integral symmetry is turned off. 8 basis functions, 48 primitive gaussians, 8 cartesian basis functions 4 alpha electrons 4 beta electrons nuclear repulsion energy 14.5519821625 Hartrees. Do NDO integrals. One-electron integrals computed using PRISM. NBasis= 8 RedAO= F NBF= 2 2 2 2 NBsUse= 8 1.00D-04 NBFU= 2 2 2 2 The question: Is G09RevA.02 is not compiled with Windows Server 2008 and/or server hardware? Any help please? Morad El-Hendawy, Ph.D. Assiut University, Egypt From owner-chemistry@ccl.net Tue Nov 28 13:03:01 2017 From: "darush aghababayee aghdar ~ gmail.com" To: CCL Subject: CCL: Special kind of hyper homologous material Message-Id: <-53078-171128125717-14844-4EoUq2eyu3tvjyCNBJt3VQ:-:server.ccl.net> X-Original-From: darush aghababayee Content-Type: multipart/alternative; boundary="001a113eda96a1ff9a055f0ebf17" Date: Tue, 28 Nov 2017 21:27:12 +0330 MIME-Version: 1.0 Sent to CCL by: darush aghababayee [aghdar#,#gmail.com] --001a113eda96a1ff9a055f0ebf17 Content-Type: text/plain; charset="UTF-8" Dear members Before I have a definition of hyper_homologous materials An example of this kind is zanjebil. --001a113eda96a1ff9a055f0ebf17 Content-Type: text/html; charset="UTF-8"
Dear members
Before I have a definition of hyper_homologous materials
An example of this kind is zanjebil.
--001a113eda96a1ff9a055f0ebf17-- From owner-chemistry@ccl.net Tue Nov 28 18:30:00 2017 From: "Leela Dodda leela.dodda|yale.edu" To: CCL Subject: CCL: LigParGen OPLS/CM1A Parameter Generator for Organic Ligands Message-Id: <-53079-171128155610-21736-JDVd0JHCfojLP2/l1hGGVA###server.ccl.net> X-Original-From: "Leela Dodda" Date: Tue, 28 Nov 2017 15:56:08 -0500 Sent to CCL by: "Leela Dodda" [leela.dodda**yale.edu] LigParGen is a web-based service that provides force field (FF) parameters for organic molecules or ligands, offered by the Jorgensen group. LigParGen provides bond, angle, dihedral, and Lennard-Jones OPLS-AA parameters with 1.14*CM1A or 1.14*CM1A-LBCC partial atomic charges. Server provides parameter and topology files for commonly used molecular dynamics and Monte Carlo packages OpenMM, Gromacs, NAMD, CHARMM, LAMMPS, CNS/X-PLOR, Q, BOSS and MCPRO. Also, the PQR file is generated. Supported input formats: SMILES, MOL and PDB. Maximum ligand size allowed is 200 atoms. You can access the server at the following link www.jorgensenresearch.com/ligpargen