From owner-chemistry@ccl.net Wed Feb 7 03:40:00 2007 From: "Carsten Detering detering__biosolveit.de" To: CCL Subject: CCL: Visualization Freeware Message-Id: <-33551-070207033702-12782-eXfyFkFbrDCD+FW6uDLh3g,,server.ccl.net> X-Original-From: "Carsten Detering" Date: Wed, 7 Feb 2007 03:36:59 -0500 Sent to CCL by: "Carsten Detering" [detering,+,biosolveit.de] Dear Young, you can use FlexV, which you can download for free from the BioSolveIT web site: http://www.biosolveit.de/download It has a PovRay ray tracer incorporated. One picture made with FlexV is this on the FlexX page for example: http://www.biosolveit.de/flexx Hope this helps, Carsten ------------------------------------------------------------------ BioSolveIT GmbH - An der Ziegelei 75 - 53757 St.Augustin - Germany Dr. Carsten Detering, Appl. Scientist detering]^[biosolveit.de Phone: +49-2241-2525-0 / Fax: -525 www.biosolveit.de > Sent to CCL by: "Young Leh" [youngleh{=}gmail.com] > > Dear CCLer, > > > > I am now looking for a visualization freeware that can be used to produce 3D molecular pictures with publishable quality. Could somebody please give me some hints? > > > > Thanks and have a great day. > > > > Young Leh> From owner-chemistry@ccl.net Wed Feb 7 06:42:00 2007 From: "Rene Thomsen rt*|*molegro.com" To: CCL Subject: CCL: Molegro Message-Id: <-33552-070207061008-15680-SaYOmtiFoITEvETWnau7Gg _ server.ccl.net> X-Original-From: "Rene Thomsen" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 7 Feb 2007 11:12:55 +0100 MIME-Version: 1.0 Sent to CCL by: "Rene Thomsen" [rt- -molegro.com] Hi, An easier way to convert proteins to ligands is to use the context menu on the specific molecule in the 'Workspace Explorer' window and select the 'Convert Protein to Ligand' option. Notice that Molegro Virtual Docker is not designed for protein-protein docking - it is mainly targeted for docking small 'drug-like' molecules. Kind regards, Rene --- Rene Thomsen Molegro Hoegh-Guldbergs Gade 10, Bldg. 1090 DK-8000 Aarhus C Denmark http://www.molegro.com On 2/7/07, Richard Leo Wood rwoodphd*|*msn.com wrote: > > Sent to CCL by: "Richard Leo Wood" [rwoodphd###msn.com] > Hi all, > > Actually, I found my own workaround, as I usually do. > > Take the peptide (as a pdb file), convert it to an xyz file. Change the unknown atoms to teh correct ones, then convert this to a mol format file. Then import the mol file into Molegro and do the docking calculations. > > Richard > > > > > From: "Richard L Wood rwoodphd{:}msn.com" > Reply-To: "CCL Subscribers" > To: "Wood, Richard L. -id3m4-" > Subject: CCL: Molegro > Date: Tue, 6 Feb 2007 18:58:02 -0500 > > Sent to CCL by: "Richard L Wood" [rwoodphd ~ msn.com] > Hi all, > > I've just started using Molegro to dock ligands to proteins and I am having some difficulty. > > I can import a protein alright, but when I import a ligand (which is a small peptide in this case), it calls it a protein. So, I have two proteins and no ligands. > > Is there a way in Molegro that I can trick it into seeing my peptide as a ligand so that I can dock it? > > TIA, > Richard From owner-chemistry@ccl.net Wed Feb 7 12:10:00 2007 From: "Richard Leo Wood rwoodphd(a)msn.com" To: CCL Subject: CCL: Molegro Message-Id: <-33553-070207120857-2747-mK/nlsIcw0zsd3wF3EGYFA . server.ccl.net> X-Original-From: "Richard Leo Wood" Date: Wed, 7 Feb 2007 12:08:53 -0500 Sent to CCL by: "Richard Leo Wood" [rwoodphd!A!msn.com] Hi all, My ligands are hexapeptides, so they are not really proteins, but I suppose could be classified as "small molecules". They are known to inhibit the receptor I am trying to "dock" them to (actually I'm trying to estimate the binding energies to the receptor). I have a concern about the results that I am getting. They don't seem to be reproducible. That is, if I run the same docking calculation over and over again, I get different results. I wonder why that is. I've noticed that the cavity sizes (for the largest cavity) vary from run to run, as well. I would think that if I used the same settings each time, I should get the same binding affinities, but I'm not. TIA, Richard Sent to CCL by: "Rene Thomsen" [rt- -molegro.com] Hi, An easier way to convert proteins to ligands is to use the context menu on the specific molecule in the 'Workspace Explorer' window and select the 'Convert Protein to Ligand' option. Notice that Molegro Virtual Docker is not designed for protein-protein docking - it is mainly targeted for docking small 'drug-like' molecules. Kind regards, Rene --- Rene Thomsen Molegro Hoegh-Guldbergs Gade 10, Bldg. 1090 DK-8000 Aarhus C Denmark http://www.molegro.com On 2/7/07, Richard Leo Wood rwoodphd*|*msn.com wrote: Sent to CCL by: "Richard Leo Wood" [rwoodphdmsn.com] Hi all, Actually, I found my own workaround, as I usually do. Take the peptide (as a pdb file), convert it to an xyz file. Change the unknown atoms to teh correct ones, then convert this to a mol format file. Then import the mol file into Molegro and do the docking calculations. Richard From owner-chemistry@ccl.net Wed Feb 7 13:43:00 2007 From: "Steve Williams willsd : appstate.edu" To: CCL Subject: CCL:G: IRC in general and in Gaussian Message-Id: <-33554-070207133452-29107-J2eiYHLNN7cRNuWjraQcSA=server.ccl.net> X-Original-From: Steve Williams Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 07 Feb 2007 13:21:37 -0500 MIME-Version: 1.0 Sent to CCL by: Steve Williams [willsd:-:appstate.edu] I am studying a series of gas phase, rather small molecule reactions. My initial investigations have shown that geometries and thermal corrections from MP2 6-31++G(d) optimizations and frequency calculations, followed by higher accuracy single point calculations gives quite nice agreement with a good deal of experimental data. Vizualization of the single imaginary frequency mode for transition state optimizations always shows a mode the appears to be the desired reaction coordinate. I have been using IRC calculations with the above MP2 method to confirm that reaction transition states connect desired reactants and products, which they seem to do. I am doing these in mass weighted coordinates in Gaussian 03, but I do not think my question is at all specific to Gaussian. My question is: How far along a reaction coordinate should an IRC be followed to confirm the connection to products and reactants? For my studies the reactant side and product side final structures (seen in a viz. program) look like they would eventually converge to the reactant or product structure. However, in most cases if I continue the IRC with too many points (or too far along the reaction coordinate) the calculation fails with an scf convergence error method. Scf=(qc,vtl) allows the IRC to go a bit farther than the default DIIS converger, but it eventually fails as well. My reactions are bimolecular with bimolecular products and the reaction coordinates are mostly H atom transfers. So, is there any general opinion out there on "how far" is "far enough" to claim that an IRC calculation demonstrates the connection from reactants to products via a transition state. Thanks for any advice. Steve Williams From owner-chemistry@ccl.net Wed Feb 7 15:21:00 2007 From: "Guilherme Menegon Arantes garantes::iq.usp.br" To: CCL Subject: CCL: soft/hardware requirements for large multiconfig. calculations Message-Id: <-33555-070207150714-22206-6dnlDDGNaP9xBOCQlmcxng]![server.ccl.net> X-Original-From: Guilherme Menegon Arantes Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 7 Feb 2007 18:06:18 -0200 MIME-Version: 1.0 Sent to CCL by: Guilherme Menegon Arantes [garantes{}iq.usp.br] Dear members, It would be interesting to know which hardware and software configurations you are using to run large active space and large basis set multiconfigurational (mainly CASSCF/CASPT2) quantum chemical computations. 64bit workstations should be a good choice nowadays, but: - how much RAM? - how much disk? What kind of disk? - any dual core issues? - any special hardware? What about software: - using MOLCAS? MOLPRO? DALTON? Other? - any code modifications? - which compiler? Any special flags? Real examples or figures (e.g., which active space run with which amount of RAM/disk) would be very helpful, too. I will sumarize the replies. Kind Regards, G -- Guilherme Menegon Arantes, PhD Sao Paulo, Brasil ______________________________________________________ From owner-chemistry@ccl.net Wed Feb 7 17:24:00 2007 From: "Block, John john.block/./oregonstate.edu" To: CCL Subject: CCL: ACS Symposium Boston August 2007 "QSAR Reborn" Message-Id: <-33556-070207144337-20933-HQIjm3o2MBQCySLsBh1tdA=-=server.ccl.net> X-Original-From: "Block, John" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C74AE7.FBBF8B77" Date: Wed, 7 Feb 2007 10:44:22 -0800 MIME-Version: 1.0 Sent to CCL by: "Block, John" [john.block_._oregonstate.edu] This is a multi-part message in MIME format. ------_=_NextPart_001_01C74AE7.FBBF8B77 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable You are encouraged to submit a paper for the symposium "QSAR Reborn: Modern QSAR Techniques and Applications - A Symposium in Memory of Dr. Phillip Magee" that will be held the during Boston American Chemical Society Meeting August 19-23, 2007. The Division of Computers in Chemistry (COMP) is the primary sponsor. =20 Organizers: Dr. Robert Clark (Tripos) bclark^-^tripos.com=20 Dr. John H. Block (Oregon State University) John.Block^-^oregonstate.edu=20 Dr. Lowell Hall (Hall Associates) halllh^-^comcast.net=20 =20 Division Co-Sponsorship: COMP (Lead sponsor) and AGRO=20 =20 Purpose: Dr. Phillip Magee was one of the pioneers in utilizing QSAR. Whereas it is common to apply this technique to bioactivities in humans, he showed its application to agrochemicals. After retiring from the Ortho Chemical Division of Standard Oil, Phil used QSAR to study transdermal properties of molecules. Until his stroke, Phil was utilizing both his knowledge of physical organic chemistry and qsar descriptors to model bioactivities. Thus, it is appropriate that a symposium in his honor include speakers who develop qsar methodologies and who apply qsar methodologies to solve problems. Phil was also the first President of the International QSAR Group and served for a number of years. An introductory speaker should give a short biography of Phil and describe his work. =20 Papers must be submitted through the ACS OASYS system at: http://oasys.acs.org/acs/234nm/comp/papers/index.cgi The deadline is April 2, 2007. =20 Topics: QSAR Descriptors Physico-chemical Topological Quantum Mechanics Geometrical/Stereochemical =20 QSAR Techniques 2D-QSAR 3D-QSAR Topological QSAR Neural networks Classification Methods =20 QSAR Applications Drug design Agrochemical design Toxicities Environmental properties =20 =20 John H. Block Phone: 541-737-5779 College of Pharmacy Fax: 541-737-3999 Oregon State University Corvallis, OR 97331 John.Block^-^oregonstate.edu blockj^-^onid.orst.edu =20 =20 ------_=_NextPart_001_01C74AE7.FBBF8B77 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

You are encouraged to submit a paper for the symposium = “QSAR Reborn:  Modern QSAR Techniques and Applications - A Symposium in = Memory of  Dr. Phillip Magee” that will be held the during Boston = American Chemical Society Meeting August 19-23, 2007.  The Division of = Computers in Chemistry (COMP) is the primary sponsor.

 

Organizers:

        Dr. Robert Clark = (Tripos)  bclark^-^tripos.com =

        Dr. John H. Block = (Oregon = State UniversityJohn.Block^-^oregonstate.edu=

        Dr. Lowell Hall (Hall Associates)  halllh^-^comcast.net =

 

Division Co-Sponsorship:

        COMP (Lead sponsor) = and AGRO

 

Purpose:<= /p>

     &nbs= p;  Dr. Phillip Magee was one of the pioneers in utilizing QSAR.  Whereas = it is common to apply this technique to bioactivities in humans, he showed its application to agrochemicals.  After retiring from the Ortho = Chemical Division of Standard Oil, Phil used QSAR to study transdermal properties = of molecules.  Until his stroke, Phil was utilizing both his knowledge = of physical organic chemistry and qsar descriptors to model = bioactivities.  Thus, it is appropriate that a symposium in his honor include speakers = who develop qsar methodologies and who apply qsar methodologies to solve = problems.  Phil was also the first President of the International QSAR Group and = served for a number of years. An introductory speaker should give a short = biography of Phil and describe his work.

 

Papers must be submitted through = the ACS OASYS system at:   http://oasy= s.acs.org/acs/234nm/comp/papers/index.cgi  The deadline is April 2, 2007.

 

Topics:

     &nbs= p;  QSAR Descriptors

     &nbs= p;          = Physico-chemical

     &nbs= p;          = Topological

     &nbs= p;          Quantum Mechanics

     &nbs= p;          = Geometrical/Stereochemical

 

     &nbs= p;  QSAR = Techniques

     &nbs= p;          = 2D-QSAR

     &nbs= p;          = 3D-QSAR

     &nbs= p;          = Topological QSAR

     &nbs= p;          Neural networks

     &nbs= p;          Classification Methods

     &nbs= p;          =

     &nbs= p;  QSAR Applications

     &nbs= p;          Drug design

     &nbs= p;          Agrochemical design

     &nbs= p;          = Toxicities

     &nbs= p;          Environmental properties

 

 

John H. = Block           &n= bsp;        Phone:  541-737-5779

College of Pharmacy    &nbs= p;    Fax:      = 541-737-3999

Oregon State University

Corvallis<= /strong>, OR 97331=

John.Block^-^oregonstate.edu=

blockj^-^onid.orst.edu

 

 

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