From owner-chemistry@ccl.net Wed Aug 11 06:08:00 2010 From: "zborowsk. .. .chemia.uj.edu.pl" To: CCL Subject: CCL:G: wave function printing Message-Id: <-42504-100811060402-14728-M3wTSdQeb4nERTqA4i74Pg .. server.ccl.net> X-Original-From: zborowsk(0)chemia.uj.edu.pl Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-2 Date: Wed, 11 Aug 2010 12:03:54 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: zborowsk.:.chemia.uj.edu.pl > Hi Krzysztof, > > The aug-cc-pvtz basis set of Ti includes g-functions, but g-functions are > not supported by the output=wfn option. > > There are two solutions to use g-functions in AIM analysis. One is to use > GAMESS(US) to generate the wavefunction file and do AIM using AIMALL. You > can also save a checkpoint file in Gaussian and then format it. AIMALL can > read it directly. > > Best, > Wenli > Thank you for interesting answer. I will try to do that. Unfortunately, this does not solve all of my problems, because I need also the wfn file for the ELF analysis. Another thing is that I expect I have no g function in the 6-311++g(3df,2p) basis set. Am I right?? Is the same with the f function?? -- http://www.youtube.com/watch?v=EXh0PT2lovk&feature=channel Krzysztof K. Zborowski Faculty of Chemistry Jagiellonian University 3 Ingardena Street 30-060 Krakow Poland phone: +48(12)632-4888 ext. 2064 or 2067 fax: +48(12)634-05-15 email: zborowsk||chemia.uj.edu.pl gg 3817259 skype kzys70 www.chemia.uj.edu.pl/~zborowsk From owner-chemistry@ccl.net Wed Aug 11 08:18:01 2010 From: "Pablo Englebienne p.englebienne__tue.nl" To: CCL Subject: CCL: PDB coordinates tranformation Message-Id: <-42505-100811052418-31471-2Fsauh+3JhF8rsUR7G7rPA(0)server.ccl.net> X-Original-From: Pablo Englebienne Content-Type: multipart/alternative; boundary="------------070005070504060004000309" Date: Wed, 11 Aug 2010 11:23:55 +0200 MIME-Version: 1.0 Sent to CCL by: Pablo Englebienne [p.englebienne__tue.nl] This is a multi-part message in MIME format. --------------070005070504060004000309 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi Gabriel, I recently used Maestro from Schrodinger (free for academics) for something similar. The key is to make a "local transformation" on all the atoms, and then re-save the file, with the new coordinate frame. For example, to align a set of atoms on a plane, you can use: alignplane plane=xy atom.sel doplanealignment There are similar functions to align atoms to an axis (alignaxis), you can browse the manual (Maestro command reference). There are also some tools on Gromacs that can re-orient structure files. Pablo Englebienne, PhD Dept. of Biomedical Engineering Dept. of Chemistry and Chemical Engineering Institute for Complex Molecular Systems (ICMS) Eindhoven University of Technology, TU/e PO Box 513, HG -1.26 5600 MB Eindhoven, The Netherlands Tel +31 40 247 5349 On 08/09/2010 03:18 PM, Gabriel Urquiza urquizagabes[A]gmail.com wrote: > Greetings CCLers. > > I am trying to make some surveys about the structures of some channel > proteins and it would really help if the Z axis coincided with the > pore of the channel and passed along the middle point among the atoms. > The problem, evidently, is that such properties are usually absent in > any PDB. So I was wondering if there would be any program able to let > me manipulate the coordinate reference of a pdb file. > > Thank you for your time. > > Gabriel Urquiza > --------------070005070504060004000309 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi Gabriel, I recently used Maestro from Schrodinger (free for academics) for something similar. The key is to make a "local transformation" on all the atoms, and then re-save the file, with the new coordinate frame.

For example, to align a set of atoms on a plane, you can use:
alignplane plane=xy atom.sel
doplanealignment
There are similar functions to align atoms to an axis (alignaxis), you can browse the manual (Maestro command reference).

There are also some tools on Gromacs that can re-orient structure files.
Pablo Englebienne, PhD
Dept. of Biomedical Engineering
Dept. of Chemistry and Chemical Engineering 
Institute for Complex Molecular Systems (ICMS)
Eindhoven University of Technology, TU/e
PO Box 513, HG -1.26
5600 MB Eindhoven, The Netherlands
Tel +31 40 247 5349

On 08/09/2010 03:18 PM, Gabriel Urquiza urquizagabes[A]gmail.com wrote:
Greetings CCLers.

I am trying to make some surveys about the structures of some channel proteins and it would really help if the Z axis coincided with the pore of the channel and passed along the middle point among the atoms. The problem, evidently, is that such properties are usually absent in any PDB. So I was wondering if there would be any program able to let me manipulate the coordinate reference of a pdb file.

Thank you for your time.

Gabriel Urquiza

--------------070005070504060004000309-- From owner-chemistry@ccl.net Wed Aug 11 08:52:01 2010 From: "Maurizio Ciofalo omega]~[unipa.it" To: CCL Subject: CCL: carbamates and MMx force fields Message-Id: <-42506-100811081606-28547-nqkkuvMI1L6HN5S86lO+2Q_._server.ccl.net> X-Original-From: "Maurizio Ciofalo" Date: Wed, 11 Aug 2010 08:16:04 -0400 Sent to CCL by: "Maurizio Ciofalo" [omega*|*unipa.it] Dear Sirs, over the last weeks I have been trying to do a conformational sampling of some carbamates by using a homemade application as well as Allinger's MMx force fields (as implemented in Tinker 5.1 package) with no success. In particular I was not able to work out molecules as simple as methyl N-methylcarbamate. It appears there are no parameters though MM3 seems to have suitable atom types for the two carbamate oxygen atoms (i.e. #75 and #90). Any suggestion on this subject? Thanks in advance Maurizio From owner-chemistry@ccl.net Wed Aug 11 11:14:00 2010 From: "Zork Zou zorkzou],[gmail.com" To: CCL Subject: CCL: wave function printing Message-Id: <-42507-100811111313-10835-MlhDo5MgI87aOVuibu+VxA^_^server.ccl.net> X-Original-From: Zork Zou Content-Type: multipart/alternative; boundary=001636e1ee15cd6431048d8dafba Date: Wed, 11 Aug 2010 09:13:05 -0600 MIME-Version: 1.0 Sent to CCL by: Zork Zou [zorkzou\a/gmail.com] --001636e1ee15cd6431048d8dafba Content-Type: text/plain; charset=ISO-8859-1 Hi Krzysztof, 6-311++g(3df,2p) also includes g-functions. You can see them using gfprint or gfinput. To the best of my knowledge, there is not a public elf program which can calculate g-functions. Wenli --001636e1ee15cd6431048d8dafba Content-Type: text/html; charset=ISO-8859-1

Hi Krzysztof,

6-311++g(3df,2p) also includes g-functions. You can see them using gfprint or gfinput.
To the best of my knowledge, there is not a public elf program which can calculate
g-functions.

Wenli

--001636e1ee15cd6431048d8dafba-- From owner-chemistry@ccl.net Wed Aug 11 13:22:01 2010 From: "David Martinsen d_martinsen|,|acs.org" To: CCL Subject: CCL: JCIM 50th Anniversary Reception and Symposium at ACS/Boston Message-Id: <-42508-100811125542-5675-+cTVjn++Y9EWoRNvyJjFpw(_)server.ccl.net> X-Original-From: "David Martinsen" Date: Wed, 11 Aug 2010 12:55:40 -0400 Sent to CCL by: "David Martinsen" [d_martinsen-x-acs.org] The Journal of Chemical Information and Modeling is turning 50, and youre invited to come celebrate with us! To observe this landmark, the Journal of Chemical Information and Modeling will have a special Symposium and Reception at the ACS Fall National, Meeting August 22-26 in Boston, Massachusetts. A joint CINF/COMP Welcoming Reception, sponsored by the Journal of Chemical Information and Modeling, will be held on Sunday, August 22, 2010 from 6:30-8:30pm at the Westin Boston Waterfront in Harbor Ballroom I. The symposium, which will feature distinguished experts from the field, will be on Monday, August 23. Confirmed speakers include: Dmitris Agrafiotis Bobby Glen Elizabeth Amin Peter Johnson Jurgen Bajorath Bill Milne Val Gillet Tudor Oprea Johnny Gasteiger Alex Tropsha Mike Gilson Peter Willett We hope to see you there! David Martinsen, ACS Publications d_martinsen.(_).acs.org Note: The COMP student and faculty awards will be taking place at the Tuesday evening poster session. From owner-chemistry@ccl.net Wed Aug 11 17:57:01 2010 From: "Andrew Orry andy]|[molsoft.com" To: CCL Subject: CCL: Protein Structure and Drug Discovery Workshop - La Jolla, CA. Sep 30 - Oct 1 Message-Id: <-42509-100811172436-17074-QluyFHLPkH394n21KjIFWQ(a)server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Wed, 11 Aug 2010 14:25:24 -0700 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy!A!molsoft.com] "Protein Structure and Drug Discovery" Workshop – Sept 30th to Oct 1st 2010 La Jolla, CA. Please join us at MolSoft's ( www.molsoft.com ) "Protein Structure and Drug Design" Workshop in La Jolla, California USA. For more information and a registration form see: www.molsoft.com/training.html This workshop is suitable for chemists and biologists who would like to learn more about computational drug discovery and bioinformatics. No prior knowledge in this field is required to participate. The workshop is presented by Prof. Ruben Abagyan (University of California San Diego) and Dr. Maxim Totrov (MolSoft). Price: $349 (Academics) $749 (Commercial) The workshops will consist of lectures, demonstrations, and "hands-on" computational experiments and will cover the following topics: - How To Display Fully Interactive 3D Molecules in PowerPoint and the Web - Sequence and Protein Structure Analysis - Protein Modeling and Simulations - Structure Validation and Optimization - Ligand Binding Site Prediction - Small Molecule Docking and Virtual Ligand Screening - Structure-based development of target-specific compound libraries - Cheminformatics, Chemical Clustering, Searching, Superposition etc... - QSAR, Machine Learning - Protein-Protein Docking Please see our website at www.molsoft.com for more details or E mail: andy]~[molsoft.com or call 858-625-2000 ext.108. For the latest MolSoft news see: http://www.molsoft.com/news.html