From owner-chemistry@ccl.net Thu Dec 24 01:22:01 2009 From: "Jio M jiomm|,|yahoo.com" <owner-chemistry[#]server.ccl.net> To: CCL Subject: CCL:G: SQM and AMBER charge trouble Message-Id: <-40959-091223005615-16028-8kYPQipGRdZwBT9ElcxU0A[#]server.ccl.net> X-Original-From: Jio M <jiomm%x%yahoo.com> Content-Type: multipart/alternative; boundary="0-802652501-1261544496=:85042" Date: Tue, 22 Dec 2009 21:01:36 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Jio M [jiomm\a/yahoo.com] --0-802652501-1261544496=:85042 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear CCL members; I am new to this group and using AMBER and GAUSSIAN I have some queries regarding AMBER and GAUSSIAN for Scaled Quantum useage. I have a large organic molecule and hence can use GAFF for that (atoms are less, antechamber can handle). I dont have problem in using hard parameters like angle, bond length of GAFF. But for dihedral torsional force constant and angle I want to derive from IR data and Scaled Quantum Mechanics (SQM) data from GAUSSIAN But the problem is : 1) I would be using some higher level theory like B3LYP for SQM and would get some charges on the atoms. For doing simulations, AMBER will use its own charges like bcc or resp that will be different from B3LYP derived in SQM. Can I use the dihedral force constants and dihedral angles from SQM, additionally in frcmod file along with GAFF (GAFF for hard parametrs). My question relate to fact that I derived dihedral force constant and=A0 angle with charges that will be different from AMBER provided charges for doing simulations, and using force const. and angle values in frcmod file. Is this OK to do like this or else I should use same charges as derived from SQM in AMBER simulations. 2) I think I cannot use resp charges, as usually suggested we should use HF= /6-31G* for esp. But I am using B3LYP method. Please suggest regarding this problem; Thanks and regards; JIomm=0A=0A=0A --0-802652501-1261544496=:85042 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable <table cellspacing=3D"0" cellpadding=3D"0" border=3D"0" ><tr><td valign=3D"= top" style=3D"font: inherit;"> Dear CCL members;<br> <br> I am new to this group and using AMBER and GAUSSIAN<br> <br> I have some queries regarding AMBER and GAUSSIAN for Scaled Quantum<br> useage.<br> I have a large organic molecule and hence can use GAFF for that (atoms<br> are less, antechamber can handle). I dont have problem in using hard<br> parameters like angle, <span class=3D"yshortcuts" id=3D"lw_1261543919_0">bo= nd length</span> of GAFF. But for dihedral torsional<br> force constant and angle I want to derive from IR data and Scaled<br> <span class=3D"yshortcuts" id=3D"lw_1261543919_1">Quantum Mechanics</span> = (SQM) data from GAUSSIAN<br> <br> But the problem is :<br> 1) I would be using some higher level theory like B3LYP for SQM and<br> would get some charges on the atoms. For doing simulations, AMBER will<br> use its own charges like bcc or resp that will be different from B3LYP<br> derived in SQM. Can I use the dihedral force constants and <span class=3D"y= shortcuts" id=3D"lw_1261543919_2">dihedral<br>angles</span> from SQM, addit= ionally in frcmod file along with GAFF (GAFF for<br> hard parametrs).<br> <br> My question relate to fact that I derived dihedral force constant<br> and angle with charges that will be different from AMBER provided<br> charges for doing simulations, and using force const. and angle values<br> in frcmod file. Is this OK to do like this or else I should use same<br> charges as derived from SQM in AMBER simulations.<br> <br> 2) I think I cannot use resp charges, as usually suggested we should use HF= /6-31G* for esp. But I am using B3LYP method.<br> <br> Please suggest regarding this problem;<br> <br> Thanks and regards;<br> JIomm</td></tr></table><br>=0A=0A=0A=0A --0-802652501-1261544496=:85042-- From owner-chemistry@ccl.net Thu Dec 24 01:57:01 2009 From: "Yosuke Kanai kanai3[]llnl.gov" <owner-chemistry*o*server.ccl.net> To: CCL Subject: CCL: Computational Chemistry and Materials Science (CCMS) Summer Institute Message-Id: <-40960-091223173816-31493-JogCPQK5nTkootXxHc970g*o*server.ccl.net> X-Original-From: "Yosuke Kanai" <kanai3(-)llnl.gov> Date: Wed, 23 Dec 2009 17:38:12 -0500 Sent to CCL by: "Yosuke Kanai" [kanai3###llnl.gov] We are pleased to announce the 2010 Computational Chemistry and Materials Science (CCMS) Summer Institute: Materials Research for Energy at the Lawrence Livermore National Laboratory (LLNL). The goal of the Summer Institute is to provide an opportunity for graduate students to explore and learn some of the cutting-edge methods in computational materials sciences, computational chemistry, and other related areas of computational science during their early years of graduate study. Each student will spend ten weeks at LLNL as the guest of an LLNL host scientist, working on a computational materials research project related to energy. In addition, renowned experts in the field from major research universities and national laboratories around the country will present a series of mini-courses for the student fellows. These courses will cover state-of-the-art and emerging computational methods in materials research for energy. There is a great deal of excitement in the computational science community for investigating various aspects of materials for energy-related problems. At the same time, there is an urgent need to train the next generation of scientists in the use of the latest computational methods and approaches for solving these challenging problems. LLNL is one of the leading national laboratories of the US Department of Energy, and is well known for its state-of-the-art computational science capabilities. Summer fellows will be selected from among an open pool of applicants who have demonstrated a strong interest in computational sciences, especially materials science and chemistry. The Institute will run from June 8 to August 13, 2010. Travel funds and a generous stipend will be provided to the participants. In order to be considered, prospective participants will need to fill out an application form that can be found at the following website: http://www.llnl.gov/ccms/ The application deadline is February 15, 2010. We would greatly appreciate it if you could bring this announcement to the attention of graduate students that you feel would benefit from the experience of hands-on research in computational chemistry and materials science, working with leading researchers at a national laboratory. Additional details about the summer institute can be found on the website listed above. Yosuke Kanai (kanai3[at]llnl.gov) Ming Tang (tang25[at]llnl.gov) Directors, CCMS Summer Institute From owner-chemistry@ccl.net Thu Dec 24 02:32:00 2009 From: "l l leonids26^gmail.com" <owner-chemistry(!)server.ccl.net> To: CCL Subject: CCL:G: software to visualize MOs Message-Id: <-40961-091222174755-24996-QxTy9zUxWtebc9MxKc3/wA(!)server.ccl.net> X-Original-From: l l <leonids26*o*gmail.com> Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 23 Dec 2009 00:54:06 +0300 MIME-Version: 1.0 Sent to CCL by: l l [leonids26]=[gmail.com] If you use Gamess or Gaussian to produce the matrix of Atomic Orbital (AO) coefficients you can use Chemissian program (http://www.chemissian.com/). It can build molecular orbitals as two-dimensional contour maps (http://www.chemissian.com/2dmap) or as one-dimensional function along a given line. Often such contour maps are much more informative than 3D isosurface! However if you want to build 3D isosurface you may choose to use e.g. Molek= el. 2009/12/22 Ana Montero analilian.montero*gmail.com <owner-chemistry],[ccl.net= >: > > Sent to CCL by: "Ana =A0Montero" [analilian.montero/a\gmail.com] > Hi members, > I want to visualize molecular orbitals (MO) from one matrix of Atomic Orb= ital (AO) coefficients. Can you suggest me some software to do it? > Thanks in advance > ana > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Thu Dec 24 16:34:01 2009 From: "sina rastegar sina_rastegar1979*_*yahoo.com" <owner-chemistry+/-server.ccl.net> To: CCL Subject: CCL:G: isotope Message-Id: <-40962-091220060119-17362-OFAb50uxbyzldyYAvZsZ6g+/-server.ccl.net> X-Original-From: "sina rastegar" <sina_rastegar1979]^[yahoo.com> Date: Sun, 20 Dec 2009 06:01:15 -0500 Sent to CCL by: "sina rastegar" [sina_rastegar1979%x%yahoo.com] I do not know how can I use an isotope in gaussian input file could anyone tell me that how can I use isotopes in gaussian 03? For example I want to use deutrium instead of hydrogen in freq computations. Thanks a lot. From owner-chemistry@ccl.net Thu Dec 24 17:10:00 2009 From: "Zhihai Liu liuhai*o*mail.sioc.ac.cn" <owner-chemistry_-_server.ccl.net> To: CCL Subject: CCL: The PDBbind database version 2009 is now released Message-Id: <-40963-091224074249-22442-HdX8MIWNneCoXK+O0thGxA_-_server.ccl.net> X-Original-From: "Zhihai Liu" <liuhai()mail.sioc.ac.cn> Date: Thu, 24 Dec 2009 07:42:45 -0500 Sent to CCL by: "Zhihai Liu" [liuhai++mail.sioc.ac.cn] Dear researchers, The PDBbind database aims at providing a comprehensive collection of experimentally measured binding affinity data for all biomolecular complexes deposited in the Protein Data Bank. Since its first public release in 2004, this database has been used by thousands of researchers all across the world. This database is now upadted annually by our group to keep up with the growth of the Protein Data Bank. Here, we are happy to announce another release of the PDBbind database, i.e. version 2009. This version provides binding affinity data and structural information for a total of 5,678 biomolecular complexes, including protein-ligand (4277), nucleic acid-ligand (44), protein-nucleic acid (304), and protein-protein complexes (1053), which is the largest collection of this kind so far. Binding data included in version 2009 have increased by 30% as compared to version 2008. All of these data are collected from original references by ourselves. They all have been double-checked to ensure that they match the complex structures in the Protein Data Bank. The PDBbind version 2009 is now available on the PDBbind-CN server at http://www.pdbbind.org.cn/. The basic information of each complex in PDBbind is totally open for browsing. Users are required to register with a license agreement if they want to use the full functions provided on our web site. Registration is free of charge to all academic and industrial users. We also love to hear your comments so that we can do a better job for next release! Best regards, Prof. Renxiao Wang Shanghai Institute of Organic Chemistry Chinese Academy of Sciences Shanghai, P. R. China From owner-chemistry@ccl.net Thu Dec 24 18:40:01 2009 From: "Daniel Jana dfjana(-)gmail.com" <owner-chemistry_._server.ccl.net> To: CCL Subject: CCL:G: isotope Message-Id: <-40964-091224183555-23137-q4FDFhQhG0FXpa+wXfOsug_._server.ccl.net> X-Original-From: Daniel Jana <dfjana!=!gmail.com> Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 24 Dec 2009 23:30:52 +0100 MIME-Version: 1.0 Sent to CCL by: Daniel Jana [dfjana ~~ gmail.com] Hello, This should help: http://www.gaussian.com/g_tech/g_ur/m_molspec.htm Cheers, Daniel sina rastegar sina_rastegar1979*_*yahoo.com wrote: > Sent to CCL by: "sina rastegar" [sina_rastegar1979%x%yahoo.com] > > > I do not know how can I use an isotope in gaussian input file > could anyone tell me that how can I use isotopes in gaussian 03? > For example I want to use deutrium instead of hydrogen in freq computations. > > Thanks a lot.> > > >