From owner-chemistry@ccl.net Tue Oct 16 02:08:01 2007 From: "=?ISO-8859-1?Q?Sina_T=FCreli?= sinatureli() gmail.com" To: CCL Subject: CCL: How to mix input geometries Message-Id: <-35387-071015203017-11905-h9m5MRM0JaVu4SYVGU/N2g{:}server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?Sina_T=FCreli?=" Content-Type: multipart/alternative; boundary="----=_Part_24206_11869822.1192490787544" Date: Tue, 16 Oct 2007 02:26:27 +0300 MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?Sina_T=FCreli?=" [sinatureli:-:gmail.com] ------=_Part_24206_11869822.1192490787544 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Well, guess different procedures can be followed using different molecular modelling tools. In spartan for example, you can first open the fixed molecule and then structurally build the undetermined molecule by hand, create a bond between them. Then you can freeze the molecule with the known geometry and apply molecular mechanics. If you check, freeze in the calculations window then only unfrozen parts will be optimized. Though keep in mind that molecular mechanics calculations are not good in cases like orbital conjugations (overlapping pi orbitals etc) so then you may have to use semi-empirical methods. Also the choice of molecular mechanics force field may affect your results. There are other tools that can do this kind of operation too. But in my experience spartan and discovery studio have the easiest to use graphical user interfaces if you want to handle the insertion of a new group via visiual interface rather editing the input file (which is also possible - and if you have the means to do so, I can advise you MOPAC2007).Though I am some what new to this field too, it may be better for you to ask for others' opinions too. Good luck On 10/15/07, Gon alo Justino goncalo.justino-#-dq.fct.unl.pt < owner-chemistry^-^ccl.net> wrote: > > > Sent to CCL by: "Gon alo Justino" [goncalo.justino]~[dq.fct.unl.pt] > Dear all, > > I'd like to hear your opinion on the following trivial procedure: how > would you build an input geometry combining a molecule with an > undetermined geometry and a group with a known and fixed geometry? An > example: taking the case of glucuronidea, I would like to use the > pre-determined structure of the glucuronide moiety and fuse it with other > geometries; besides the copy/paste procedure, are there any alternatives? > > Thanks in advance to all, > Gonalo Justino> > > > ------=_Part_24206_11869822.1192490787544 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Well, guess different procedures can be followed using different molecular = modelling tools. In spartan for example, you can first open the fixed molec= ule and then structurally build the undetermined molecule by hand, create a= bond between them. Then you can freeze the molecule with the known geometr= y and apply molecular mechanics. If you check, freeze in the calculations w= indow then only unfrozen parts will be optimized. Though keep in mind that = molecular mechanics calculations are not good in cases like orbital conjuga= tions (overlapping pi orbitals etc) so then you may have to use semi-empiri= cal methods. Also the choice of molecular mechanics force field may affect = your results. There are other tools that can do this kind of operation too.= But in my experience spartan and discovery studio have the easiest to use = graphical user interfaces if you want to handle the insertion of a new grou= p via visiual interface rather editing the input file (which is also possib= le - and if you have the means to do so, I can advise you MOPAC2007).Though= I am some what new to this field too, it may be better for you to ask for = others' opinions too. Good luck

On 10/15/07, Gon alo Justino goncalo.justino-#-dq.fct.unl.pt <owner-chemistry^-^ccl.net> wrote:

Sent to CCL b= y: "Gon  alo  Justino" [goncalo.justino]~[ dq.fct.unl.pt]
Dear all,

I'd like to hear your opinion on= the following trivial procedure: how would you   build an input = geometry combining a molecule with an undetermined geometry and a group wit= h a known and fixed geometry? An example: taking the case of glucuronidea, = I would like to use the pre-determined structure of the glucuronide moiety = and fuse it with other geometries; besides the copy/paste procedure, are th= ere any alternatives?

Thanks in advance to all,
Gonalo Justino



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------=_Part_24206_11869822.1192490787544-- From owner-chemistry@ccl.net Tue Oct 16 07:53:00 2007 From: "J.Aires de Sousa jas!^!fct.unl.pt" To: CCL Subject: CCL: computer aided drug design course / cheminformatics teaching material Message-Id: <-35388-071016071452-25536-blmwIXlZWwMdPzxhHfSJ2w!^!server.ccl.net> X-Original-From: "J.Aires de Sousa" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 16 Oct 2007 11:14:38 +0100 MIME-Version: 1.0 Sent to CCL by: "J.Aires de Sousa" [jas]~[fct.unl.pt] You may be interested in this teaching material for a course of chemoinformatics: http://www.dq.fct.unl.pt/staff/jas/qc It includes slides, exercises, and the required resources for the exercises (files, data sets, links to free web services, and links to available software). Slides are in pdf format. For the ppt files please contact me. -- Prof. Joao Aires de Sousa Departamento de Quimica, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal Tel: (+351) 21 2948300 x10986 Fax: (+351) 21 2948550 Email: jas_at_fct.unl.pt www: http://www.dq.fct.unl.pt/staff/jas/ >Dear ccl users, >I would like to give a "computer aided drug design" course for the 5th >year pharmacy students. >Any suggestions concerning the course, materials, software, lectures >notes, ppt and others. >Thanks in advance > >Dr. Omar Deeb >Al-Quds University >Jerusalem From owner-chemistry@ccl.net Tue Oct 16 08:37:01 2007 From: "aps1968^googlemail.com" To: CCL Subject: CCL: (re-)relaxing molecules Message-Id: <-35389-071016040242-13703-CM+jN/Zc8FaWSvYSsaUUrg-,-server.ccl.net> X-Original-From: aps1968(!)googlemail.com Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 16 Oct 2007 10:02:30 +0200 MIME-Version: 1.0 Sent to CCL by: aps1968,,googlemail.com Vladimir, Thank you for your reply. My question however was more precise, so I would like to encourage all of you to refer to it. Sincerely, Andy 2007/10/13, chupvl chupvl~!~gmail.com : > > Sent to CCL by: chupvl [chupvl|gmail.com] > Hello! > > In my point there three main ways of 3D alignment of the molecules > > - point-2-point matching as in MATCH potion of Sybyl > - pharmacophoric matching > - receptor-based alignment (You'll be using MATCH option after docking > of series of molecules) > > and one more (I don't met an article about this but I think it's exist - > is molecular descriptors alignment after descriptors selection based eg > on good QSAR model) > > Vladimir Chupakhin > MSU, Dpt. of Chemistry, > Moscow, Russia > > > > aps1968**googlemail.com wrote: > > Sent to CCL by: aps1968*|*googlemail.com > > Dear CClrs, > > > > in order to perform CoMFA computations in Sybyl, I aligned my already > > externally optimized molecules with the use of the function MATCH, taking > > into account the fragment common for all molecules. The referee of the paper > > however asks if the molecules were re-relaxed after the MATCH procedure. > > I am not quite sure I understand what he means. Should I again in the > > new positions perform any further optimization? They are already > > optimized. He also > > suggests a pharmacofore based alignment prior to comfa and again asks to > > consider relaxing the conformers after MATCH alignment prior to comfa. > > Any comments to that? Which alternative alignment methods can be > > recommended to a SYBYL user? > > > > Regards, > > > > Andy> > > > From owner-chemistry@ccl.net Tue Oct 16 09:27:00 2007 From: "Wolfram Altenhofen wolfram(~)chemcomp.com" To: CCL Subject: CCL: Hands-on MOE Training Session at upcoming CIC Conference in Goslar Message-Id: <-35390-071016092255-11390-V3d4n1TmY2r55b/z+h+w1g+*+server.ccl.net> X-Original-From: "Wolfram Altenhofen" Date: Tue, 16 Oct 2007 09:22:51 -0400 Sent to CCL by: "Wolfram Altenhofen" [wolfram_+_chemcomp.com] CCG is pleased to offer a free hands-on session introducing new features of the 2007.09 release of the Molecular Operating Environment (MOE) on the occasion of the 21. CIC conference in Goslar organized by GDCh (http://www.gdch.de/vas/tagungen/tg/5316__e.htm). The market place session will take place on Sun 11th of November at the conference venue "Hotel Achtermann" in Goslar between 2 and 5 pm. The tutorial will guide through new technology availble in the 2007.09 release of MOE including: - a scaffold replacement methodology integrated with existing Pharmacophore Discovery tools - a very fast and accurate method to assign ionization states and proton geometries in macromolecules - pipelining tools for tautomer and ionization state enumeration of small molecules - interactive structure-based ligand optimization for medicinal chemists - enhanced Ligand Receptor docking and an interface to BioSolveIT's FlexS docking engine. If you are interested in participating, please contact Dr. Wolfram Altenhofen Director of Scientific Services Chemical Computing Group AG Kaiser-Wilhlem-Ring 11 50672 Kln Germany wolfram-#-chemcomp.com From owner-chemistry@ccl.net Tue Oct 16 11:56:01 2007 From: "Oellien, F (Frank) Frank.Oellien**Intervet.com" To: CCL Subject: CCL: German Conference on Chemoinformatics - Final Call for Registration Message-Id: <-35391-071016115459-14902-gccLWVHxExQ0RrOUIeEBBw-*-server.ccl.net> X-Original-From: "Oellien, F (Frank)" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 16 Oct 2007 17:04:23 +0200 MIME-Version: 1.0 Sent to CCL by: "Oellien, F (Frank)" [Frank.Oellien^-^Intervet.com] The CIC division of the German Chemical Society would kindly remember = you that the official registration period for the 3. German Conference = on Chemoinformatics (http://www.gdch.de/gcc2007) (Goslar, Germany, = November 11-13, 2007) will end on October 21, 2007. Only participants = that register through our online registration form = (http://www.gdch.de/vas/tagungen/tg/5316/regist.htm) until this date = will still be listed in the abstract book.=20 A registration after October, 21 is still possible for the same = registration fees, however we can not mention these people in the = abstract book (list of participants) anymore. The conference will address a broad range of modern research topics in = the field of Computers and Chemistry. Focus will be on recent = developments and trends in the fields of * Chemoinformatics and Drug Development * Chemical Information * Molecular Modelling * Computational Material Science and Nanotechnology The complete scientific program is available as HTML = (http://www.gdch.de/vas/tagungen/tg/5316/program.htm) and PDF = (http://scholle.oc.uni-kiel.de/users/cic/tagungen/workshop07/GCC_Programm= _2007.pdf). We also want to draw your attention to the free software tutorials = (several Open Source groups) and the two market place events by Accelrys = (Introduction to data workflows for research informatics through = Pipeline Pilot and Accord) and Chemical Computing Group (Hands-on = introduction to new applications in MOE 2007) on Sunday afternoon (2pm - = 5pm) Abstracts for last minute posters can still be submitted until November = 5. However, these contributions can also not be mentioned in the = abstract book anymore. Hope to see you in Goslar. With kind regards =20 Dr. Frank Oellien Scientist Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany =20 E-Mail: frank.oellien(~)intervet.com Phone: +49 (6130) 948 365 Fax: +49 (6130) 948 517 Home http://www.intervet.com =20 Intervet Innovation GmbH is an Akzo Nobel company =20 Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 = Gesch=E4ftsf=FChrer: Dr. Peter Schmid =20 -------------------------------------- This message, including attachments, is confidential and may be privileged. If you are not an intended recipient, please notify the sender then delete and destroy the original message and all copies. You should not copy, forward and/or disclose this message, in whole or in part, without permission of the sender. -------------------------------------- From owner-chemistry@ccl.net Tue Oct 16 12:33:01 2007 From: "Diederica Claeys diederica.claeys-$-gmail.com" To: CCL Subject: CCL:G: g03 NMR(ReadAtoms) Message-Id: <-35392-071016122009-26594-wBzRzJXyANFlptQ3dmwg1g a server.ccl.net> X-Original-From: "Diederica Claeys" Date: Tue, 16 Oct 2007 12:20:06 -0400 Sent to CCL by: "Diederica Claeys" [diederica.claeys|*|gmail.com] Dear CCLrs, I have problems with the input-file for Gaussian03 to calculate spin-spin coupling constants for specific atoms. The input I used was: %nproc=4 %chk=spinreadatoms.chk p b3lyp/6-311+g* NMR=(SpinSpin,ReadAtoms) gfinput spin 0 1 O 0.000000 0.000000 0.000000 C 0.000000 0.000000 1.443984 . . . H 0.730228 3.426591 4.880223 18 21 Without the readatoms command the calculation starts, but after specifying atoms it doesn't. Does anyone has experience with this? Thanks in advance, Diederica Claeys diederica.claeys[-]gmail.com From owner-chemistry@ccl.net Tue Oct 16 15:34:01 2007 From: "Lee R Shekter lshekter=transitiontherapeutics.com" To: CCL Subject: CCL: computer aided drug design course / cheminformatics teaching material Message-Id: <-35393-071016133311-3575-Mo6mZM+3VSUDMPpi0b+l2Q||server.ccl.net> X-Original-From: "Lee R Shekter" Date: Tue, 16 Oct 2007 13:33:08 -0400 Sent to CCL by: "Lee R Shekter" [lshekter(a)transitiontherapeutics.com] You may also try Molecular Conceptor, from Synergix. Their website is http://www.molecular-conceptor.com. A possible advantage for you is that Synergix is located in your vicinity. Lee Shekter Scientist, Molecular Modeling Transition Therapeutics, Inc. Toronto, Canada > "J.Aires de Sousa jas!^!fct.unl.pt" wrote: > > Sent to CCL by: "J.Aires de Sousa" [jas]~[fct.unl.pt] > You may be interested in this teaching material for a course of > chemoinformatics: > http://www.dq.fct.unl.pt/staff/jas/qc > > It includes slides, exercises, and the required resources for the > exercises (files, data sets, links to free web services, and links to > available software). > > Slides are in pdf format. For the ppt files please contact me. > -- > Prof. Joao Aires de Sousa > Departamento de Quimica, Faculdade de Ciencias e Tecnologia, > Universidade Nova de Lisboa, 2829-516 Caparica, Portugal > Tel: (+351) 21 2948300 x10986 Fax: (+351) 21 2948550 > Email: jas_at_fct.unl.pt > www: http://www.dq.fct.unl.pt/staff/jas/ > > >Dear ccl users, > >I would like to give a "computer aided drug design" course for the 5th > >year pharmacy students. > >Any suggestions concerning the course, materials, software, lectures > >notes, ppt and others. > >Thanks in advance > > > >Dr. Omar Deeb > >Al-Quds University > >Jerusalem > >