From owner-chemistry@ccl.net Thu Jan 31 00:42:01 2008 From: "Seth Olsen s.olsen1-*-uq.edu.au" To: CCL Subject: CCL: Project molecular geometry into symmetry point group? Message-Id: <-36168-080130233209-3232-BRink3/013M4xDPeIkHXUg(0)server.ccl.net> X-Original-From: Seth Olsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 31 Jan 2008 13:47:15 +1000 MIME-Version: 1.0 Sent to CCL by: Seth Olsen [s.olsen1#%#uq.edu.au] Hi CCL'ers, I have a molecular geometry that is very close to C3 symmetry, but apparently is not. The molecule is large, so it is going to take a prohibitively long time to sort through all the bonds, angles, etc. Can anyone point me to a software package that I can use to project the geometry into the right symmetry group? Even better would be a package that also would tell me just how big the alteration is upon making it. Cheers, Seth -- &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& Dr Seth Olsen, PhD Postdoctoral Fellow, Biomolecular Modeling Group Centre for Computational Molecular Science Australian Institute of Bioengineering and Nanotechnology (75) The University of Queensland Qld 4072, Brisbane, Australia tel (617) 3346 3976 fax (617) 3365 4623 email: s.olsen1() uq.edu.au Web: www.ccms.uq.edu.au &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& The opinions expressed here are my own and do not represent the official position of the University of Queensland, its trustees or subsidiaries. From owner-chemistry@ccl.net Thu Jan 31 02:59:00 2008 From: "=?iso-8859-1?Q?Mads_N=F8rregaard-Madsen?= MN * nuevolution.com" To: CCL Subject: CCL: CRT monitors for hardware stereo Message-Id: <-36169-080129155704-19908-mDOhVA78g9bRXxIRDFDMQw*server.ccl.net> X-Original-From: =?iso-8859-1?Q?Mads_N=F8rregaard-Madsen?= Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 29 Jan 2008 21:24:11 +0100 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-1?Q?Mads_N=F8rregaard-Madsen?= [MN * nuevolution.com] Hi, It might be worth considering the newly announced range of 3D LCD = monitors from Zalman = (http://www.zalman.com/ENG/product/CategorySecond_Pic.asp?categoryname=3D= Monitors&categorySecond=3D). Seems to be the most serious alternative to = 3D capable CRT monitors. Does anybody have experience with these? Best regards, Mads Mads N=F8rregaard-Madsen Nuevolution A/S -----Original Message----- > From: owner-chemistry . ccl.net [mailto:owner-chemistry . ccl.net]=20 Sent: Tuesday, January 29, 2008 1:55 PM To: Mads N=F8rregaard-Madsen Subject: CCL: CRT monitors for hardware stereo Sent to CCL by: "Pieter Stouten" [Pieter.Stouten:+:glpg.com] I am looking for monitors for use with hardware stereo. I used to use the Samsung SyncMaster 1100DF and I was very happy with it. A colleague recommended the NEC-Mitsubishi FP2141SB. Unfortunately, both seem to have been discontinued. To have an adequate refresh rate and no ghost images, the rule of thumb was that only a CRT monitor would do. Is that still the case? If you have good hardware stereo experiences with a specific monitor (CRT or otherwise), could you please let me know? And what stereo-emitter and stereo-glasses work well for you? Any opinions, hints or pointers are much appreciated. And yes, in case you were wondering, we do have job openings: http://www.glpg.com/careers/openings.htm http://www.ccl.net/cca/jobs/joblist/mess0011231.shtml Thanks, Pieter Pieter Stouten Group Leader Computational Chemistry Galapagos NV, Mechelen, Belgium -- This e-mail and its attachment(s) (if any) may contain confidential = and/or proprietary information and is intended for its addressee(s) = only. Any unauthorized use of the information contained herein = (including, but not limited to, alteration, reproduction, communication, = distribution or any other form of dissemination) is strictly prohibited. = If you are not the intended addressee, please notify the orginator = promptly and delete this e-mail and its attachment(s) (if any) = subsequently.=20 Galapagos nor any of its affiliates shall be liable for direct, special, = indirect or consequential damages arising from alteration of the = contents of this message (by a third party) or as a result of a virus = being passed on. -=3Dhis is automatically added to each message by the mailing script =3Dhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20Search Messages: http://www.ccl.net/htdig (login: ccl, Password: = search)http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Jan 31 05:51:00 2008 From: "willsd-x-appstate.edu" To: CCL Subject: CCL:G: problem with aim calculation Message-Id: <-36170-080131051448-18630-XBv5HLGA0HiSTcUJNgXKWg|server.ccl.net> X-Original-From: Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Thu, 31 Jan 2008 09:37:30 GMT MIME-Version: 1.0 Sent to CCL by: [willsd]*[appstate.edu] I have been watching this aim discussion for a few days and I may have a useful suggestion. With previous versions (g98 and maybe before that) the .wfn file would be created when output=wfn was specified in the route line, a suitable file name specified at the end of the input (as nicely described below), AND punch=archive was also included in the route line. I do not know if punch=archive is still needed, but I do know that it still works with g03. As others have mentioned I also recommend density=current and scf=tight (for single point calculation). After seeing it mentioned here I have also tried aimall and found it to be significantly faster than I expected. Steve Williams ----- Original Message ----- > From: "N. Sukumar nagams:_:rpi.edu" Date: Wednesday, January 30, 2008 8:05 pm Subject: CCL:G: problem with aim calculation To: "Williams, Steve " > > Sent to CCL by: "N. Sukumar" [nagams-,-rpi.edu] > The AIM keyword has nothing to do with the generation of the WFN file. > Writing the WFN file is controlled by the OUT=WFN keyword, which > specifies that a WFN file is to be written out to the file name > specified > in the com file after the coordinate section. Did you remember to > terminate the com file with the name of the WFN file to be written > out?For example... > > ...coordinate section... > > test.wfn > > This will write out a test.wfn file. If you check the end of your log > file (after the chk punch file and just before the random > quotation) you > will see something like: > Writing a WFN file to test.wfn. > > If you didn't specify a WFN file name to write to, this will look > like:Writing a WFN file to . > because there was nowhere to write the WFN file to and g03 probably > dumped your wfn to /dev/null! > > N. Sukumar > Associate Research Professor of Chemistry and Chemical Biology > Center for Biotechnology and Interdisciplinary Studies > Rensselaer Polytechnic Institute > http://reccr.chem.rpi.edu/ > ==============Original message text=============== > On Wed, 30 Jan 2008 16:46:26 EST "Abdeladim guermoune > lguermoune#hotmail.com" wrote: > > > Sent to CCL by: "Abdeladim guermoune" [lguermoune!=!hotmail.com] > Dear members, > I have use the suggested instruction : > #P B3P86 6-311++G(3DF,2P) DENSITY=CURRENT SCF=(TIGHT,SAVE) > ouTPUT=WFN SCFCYC=250 > Without aim keyword, so the wfn file is empty. > Lets remember that the calculation is realized with G03 (version > D). The > earlier attempts abort with error : THE MOLECULAR GRAPH IS > DISCONNECTED... ABORTING! And again when I try the work as > suggested : #p B3P86 > 6-311++G(3df,2p) aim=all density=current scf=(tight,save) output=wfn > scfcyc=250 guess=huckel 6d 10f > I hope that the AIMQB program give the solution as proposed, when > the chk > file is treated by the program, so any additional keyword in order > to get > the best chk? > All suggestions are welcome. > And thanks for your help. > > Guermoune.http://www.ccl.net/cgi- > bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text=========== > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > changethe strange characters on the top line to the .|. sign. You can > also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > > From owner-chemistry@ccl.net Thu Jan 31 07:54:00 2008 From: "Raji Raji raji|a|anal.chem.tohoku.ac.jp" To: CCL Subject: CCL:G: CIS-Optimization of first excited state Message-Id: <-36171-080131075231-3858-U8S5dE6NcecHXrJ3Sk0TsA^^server.ccl.net> X-Original-From: "Raji Raji" Date: Thu, 31 Jan 2008 07:52:27 -0500 Sent to CCL by: "Raji Raji" [raji .. anal.chem.tohoku.ac.jp] Dear CCL Members, My CIS-optimization of first excited state calculation terminated with error. Please find the part of the input and output files below. There is some problem in finalizing the calculation and writing the output. But I dont know how to solve it. Any help will be greatly acknowledged. Thanks in advance. INPUT FILE: #CIS(Root=1, Direct)/6-31+G(d) opt Pop=full gfprint SCRF=(CPCM, Read, Solvent=Water) optimization of first excited state 1 1 7 -0.066331 0.012768 -0.911231 6 -0.892347 0.716259 -1.667179 ............ OUTPUT FILE: Error termination request processed by link 9999. Error termination via Lnk1e in /usr/ap/g03/l9999.exe at Thu Jan 31 13:56:47 2008. Job cpu time: 0 days 11 hours 37 minutes 30.9 seconds. From owner-chemistry@ccl.net Thu Jan 31 08:28:00 2008 From: "ilhan yavuz ilhanyav{}gmail.com" To: CCL Subject: CCL:G: G3(MP2)-RAD cals. Message-Id: <-36172-080131082117-17965-OmW3bCUamkvS2Pm5JOKwkA _ server.ccl.net> X-Original-From: "ilhan yavuz" Date: Thu, 31 Jan 2008 08:21:13 -0500 Sent to CCL by: "ilhan yavuz" [ilhanyav!A!gmail.com] Dear CCL.NET people, Does anyone know how to build an input file for G3(MP2)-RAD calculation in Gaussian ? thank you. ilhan From owner-chemistry@ccl.net Thu Jan 31 10:20:00 2008 From: "Modelling & Design of Molecular Materials mdmm]|[mml.ch.pwr.wroc.pl" To: CCL Subject: CCL: Modelling & Design of Molecular Materials 2008 Message-Id: <-36173-080131041800-1368-FTT/jzTaM4V1Jhu/A8Neyw[*]server.ccl.net> X-Original-From: Modelling & Design of Molecular Materials Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 31 Jan 2008 09:17:59 +0100 MIME-Version: 1.0 Sent to CCL by: Modelling & Design of Molecular Materials [mdmm!^!mml.ch.pwr.wroc.pl] Dear CCL subscribers, Registration is now open for Modelling and Design of Molecular Materials 2008, which will take place in Piechowice, Poland, June 23-28, 2008. Online registration and more information is avaiable at the conference web page: http://mml.ch.pwr.wroc.pl/mdmm2008 Modelling and Design of Molecular Materials is a biannual conference devoted to presenting contemporary computational methods along with their applications in molecular modelling and molecular material design and related fields. Planned sessions include: * catalyst design * drug design * design of materials for electronics * new computational methods * structural genomics * biopolymer structure prediction * modelling chemical reactions * modeling intermolecular interactions All conference lectures during the 2008 edition of MDMM will be held in Piechowice at the Hotel "Las", about 150 kilometers from Wrocaw in the Karkonosze Mountains. Refereed conference proceedings will be published in the Journal of Molecular Modeling. Proceedings from previous conferences can be found in the same journal - in the July 2007 issue from MDMM 2006 and in the September 2005 issue from MDMM 2004. Some contributions from the 2004 meeting have also appeared in the Springer book volume Molecular Materials with Specific Interactions: Modeling & Design. MDMM 2008 is a meeting organized by: Wrocaw University of Technology (MMQC), Wrocaw, Poland Wrocaw Center for Networking and Supercomputing, Wrocaw, Poland Wrocaw Research Centre EIT+, Wrocaw, Poland Jackson State University, Jackson, MS, USA Charles University in Prague, Czech Republic Hope to see you in Piechowice, W.A. Sokalski, MDMM 2008 Chair -- Modelling and Design of Molecular Materials 2008 June 23-28 - Piechowice, Poland Conference webpage: http://www.mml.ch.pwr.wroc.pl/mdmm2008 From owner-chemistry@ccl.net Thu Jan 31 10:55:00 2008 From: "Ulrich Scharfenort scharfenort-x-ltt.rwth-aachen.de" To: CCL Subject: CCL:G: CIS-Optimization of first excited state Message-Id: <-36174-080131100547-24856-R1aK4A4d99X4ldxXNJHngw||server.ccl.net> X-Original-From: Ulrich Scharfenort Content-transfer-encoding: 7BIT Content-type: text/plain; charset=ISO-8859-15 Date: Thu, 31 Jan 2008 15:35:29 +0100 MIME-version: 1.0 Sent to CCL by: Ulrich Scharfenort [scharfenort|*|ltt.rwth-aachen.de] Dear Colleague, I had the same problem once in the past this text from the net helped me. There are many reasons caused by this error. Usually, this error shows that the iteration is not convergence. First, check the maximum iteration number, if it is exceed the number, means the iteration is not yet finish. You can repeat the iteration from the latest geometry with keyword /Geom=check/ and add /maxcyc=100/ for example. best wishes Ulrich Scharfenort Raji Raji raji|a|anal.chem.tohoku.ac.jp schrieb: > Sent to CCL by: "Raji Raji" [raji .. anal.chem.tohoku.ac.jp] > Dear CCL Members, > My CIS-optimization of first excited state calculation terminated with error. Please find the part of the input and output files below. There is some problem in finalizing the calculation and writing the output. But I dont know how to solve it. Any help will be greatly acknowledged. Thanks in advance. > > INPUT FILE: > > #CIS(Root=1, Direct)/6-31+G(d) opt Pop=full gfprint SCRF=(CPCM, Read, Solvent=Water) > > optimization of first excited state > > 1 1 > 7 -0.066331 0.012768 -0.911231 > 6 -0.892347 0.716259 -1.667179 > ............ > > > OUTPUT FILE: > > Error termination request processed by link 9999. > Error termination via Lnk1e in /usr/ap/g03/l9999.exe at Thu Jan 31 13:56:47 2008. > Job cpu time: 0 days 11 hours 37 minutes 30.9 seconds.> > > > From owner-chemistry@ccl.net Thu Jan 31 15:22:01 2008 From: "Mariusz Radon mariusz.radon/a\gmail.com" To: CCL Subject: CCL:G: CIS-Optimization of first excited state Message-Id: <-36175-080131140138-17537-8/WzycO4goSwA5htEffBXA]~[server.ccl.net> X-Original-From: "Mariusz Radon" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 31 Jan 2008 19:06:08 +0100 MIME-Version: 1.0 Sent to CCL by: "Mariusz Radon" [mariusz.radon#%#gmail.com] By placing "P" at the beginning of the route section [i.e. "#P CIS (...)"] you will get more verbose output. So you will be able to find out what exactly is going wrong during the calculation. best regards, Mariusz > INPUT FILE: > > #CIS(Root=1, Direct)/6-31+G(d) opt Pop=full gfprint SCRF=(CPCM, Read, Solvent=Water) > > optimization of first excited state > > 1 1 > 7 -0.066331 0.012768 -0.911231 > 6 -0.892347 0.716259 -1.667179 > ............ > > > OUTPUT FILE: > > Error termination request processed by link 9999. > Error termination via Lnk1e in /usr/ap/g03/l9999.exe at Thu Jan 31 13:56:47 2008. > Job cpu time: 0 days 11 hours 37 minutes 30.9 seconds. > From owner-chemistry@ccl.net Thu Jan 31 16:09:00 2008 From: "Manali Joshi manali%%adrik.bchs.uh.edu" To: CCL Subject: CCL: Freeware for protein-small molecule minimization Message-Id: <-36176-080131160245-31579-DVMxo+VvKt/9Yf3LRP6dkQ~~server.ccl.net> X-Original-From: "Manali Joshi" Date: Thu, 31 Jan 2008 16:02:42 -0500 Sent to CCL by: "Manali Joshi" [manali**adrik.bchs.uh.edu] Hi, I have a protein and a list of thousands of small molecules in the appropriate binding orientation. I want to be able to perform energy minimization of the binding site of the protein with each small molecule (using semi-empirical or similar charges). I am looking for freeware that can automate this process. Any help will be greatly appreciated. Thanks Manali From owner-chemistry@ccl.net Thu Jan 31 16:38:01 2008 From: "Kalju Kahn kalju],[chem.ucsb.edu" To: CCL Subject: CCL: Project molecular geometry into symmetry point group? Message-Id: <-36177-080131155048-13339-UfkgLw0gPYi/nBhRb7yUsA#,#server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 31 Jan 2008 12:50:30 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju[]chem.ucsb.edu] Dear Seth, I found SYMMOL easy to use. A python script that facilitates the conversion of MDL MOL files to the symmetric gamess input wia SYMMOL is available from: http://www.chem.ucsb.edu/~kalju/chem226/public/pcgamess_tutorial_A2.html Best regards, Kalju ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry, UC Santa Barbara, CA 93106 > > Sent to CCL by: Seth Olsen [s.olsen1#%#uq.edu.au] > > Hi CCL'ers, > > I have a molecular geometry that is very close to C3 symmetry, but > apparently is not. The molecule is large, so it is going to take a > prohibitively long time to sort through all the bonds, angles, etc. Can > anyone point me to a software package that I can use to project the > geometry into the right symmetry group? Even better would be a package > that also would tell me just how big the alteration is upon making it. > > Cheers, > > Seth > > -- > &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& > > Dr Seth Olsen, PhD > Postdoctoral Fellow, Biomolecular Modeling Group > Centre for Computational Molecular Science > Australian Institute of Bioengineering and Nanotechnology (75) > The University of Queensland > Qld 4072, Brisbane, Australia > > tel (617) 3346 3976 > fax (617) 3365 4623 > email: s.olsen1|-|uq.edu.au > Web: www.ccms.uq.edu.au > > &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& > The opinions expressed here are my own and do not represent the official > position of the University of Queensland, its trustees or subsidiaries.> > > From owner-chemistry@ccl.net Thu Jan 31 17:26:01 2008 From: "Greg Warren greg]~[eyesopen.com" To: CCL Subject: CCL: Freeware for protein-small molecule minimization Message-Id: <-36178-080131170556-14938-STdvdGzwO2XglisF9/FbVA---server.ccl.net> X-Original-From: Greg Warren Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 31 Jan 2008 15:05:47 -0700 MIME-Version: 1.0 Sent to CCL by: Greg Warren [greg^-^eyesopen.com] Dear Manali, Szybki, an optimization program by OpenEye that will perform that task you are trying to do. Szybki takes a protein and a list of ligands and will optimize the ligand conformation in the presence of a rigid protein, protein with flexible side chains, or protein with flexible polar hydrogens. Szybki has a number of electrostatic models that can be used during optimization as well. Last, all of OpenEye software is available free of charge to academic researchers. Please see the attached link to obtain a license for Szybki. - http://www.eyesopen.com/forms/academic_license_app.php. Additional information about the software can be found at http://www.eyesopen.com/docs/ Regards, Greg Manali Joshi manali%%adrik.bchs.uh.edu wrote: > Sent to CCL by: "Manali Joshi" [manali**adrik.bchs.uh.edu] > Hi, > > I have a protein and a list of thousands of small molecules in the appropriate binding orientation. I want to be able to perform energy minimization of the binding site of the protein with each small molecule (using semi-empirical or similar charges). > I am looking for freeware that can automate this process. > Any help will be greatly appreciated. > > Thanks > Manali> > > -- ======================================== Gregory Warren, PhD OpenEye Scientific Software, Inc 9 Bisbee Court, Suite D Santa Fe, NM 87508 (505) 473-7385 ext 50 mailto:greg_-_eyesopen.com ======================================== From owner-chemistry@ccl.net Thu Jan 31 18:26:01 2008 From: "Adam Tenderholt atenderholt() gmail.com" To: CCL Subject: CCL: Project molecular geometry into symmetry point group? Message-Id: <-36179-080131150515-27342-fPNVwnI90/1JvIOgJRz+tg-*-server.ccl.net> X-Original-From: "Adam Tenderholt" Content-Type: multipart/mixed; boundary="----=_Part_3658_611816.1201806040105" Date: Thu, 31 Jan 2008 11:00:40 -0800 MIME-Version: 1.0 Sent to CCL by: "Adam Tenderholt" [atenderholt#,#gmail.com] ------=_Part_3658_611816.1201806040105 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Seth, If you have access to a computer with Python with Numeric, the attached python script will rotate a molecule around the Z axis. Currently it's set to rotate by 120 degrees. Make sure that the atoms in each of the three "pieces" are consecutive or this won't really save you much time. Next, make sure to center your molecule and align the C3 axis along the Z axis, and then call this script twice. First, rotate your structure by 120 and then (second) rotate that result by another 120 degrees. You can then use a spreadsheet program to "average" the structures, making sure that you only rearrange the "pieces" so that the coordinates basically match---otherwise, you get a really weird structure. Hope this helps, Adam -- Adam Tenderholt http://qmforge.sourceforge.net On Jan 30, 2008 7:47 PM, Seth Olsen s.olsen1-*-uq.edu.au wrote: > > Sent to CCL by: Seth Olsen [s.olsen1#%#uq.edu.au] > > Hi CCL'ers, > > I have a molecular geometry that is very close to C3 symmetry, but > apparently is not. The molecule is large, so it is going to take a > prohibitively long time to sort through all the bonds, angles, etc. Can > anyone point me to a software package that I can use to project the > geometry into the right symmetry group? Even better would be a package > that also would tell me just how big the alteration is upon making it. > > Cheers, > > Seth > > -- > &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& > > Dr Seth Olsen, PhD > Postdoctoral Fellow, Biomolecular Modeling Group > Centre for Computational Molecular Science > Australian Institute of Bioengineering and Nanotechnology (75) > The University of Queensland > Qld 4072, Brisbane, Australia > > tel (617) 3346 3976 > fax (617) 3365 4623 > email: s.olsen1|-|uq.edu.au > Web: www.ccms.uq.edu.au > > &&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&&& > The opinions expressed here are my own and do not represent the official position of the University of Queensland, its trustees or subsidiaries.> > > ------=_Part_3658_611816.1201806040105 Content-Type: application/octet-stream; name=rotate.py Content-Transfer-Encoding: base64 X-Attachment-Id: f_fc3o93560 Content-Disposition: attachment; filename=rotate.py IyEvdXNyL2Jpbi9lbnYgcHl0aG9uCgppbXBvcnQgTnVtZXJpYwppbXBvcnQgc3lzCmZyb20gbWF0 aCBpbXBvcnQgcGksIGNvcywgc2luCgphbmdsZSA9IDEyMAoKZmlsZSA9IG9wZW4oc3lzLmFyZ3Zb MV0pCnNpemUgPSBpbnQoZmlsZS5yZWFkbGluZSgpKQplbXB0eSA9IGZpbGUucmVhZGxpbmUoKQoK YXRvbWNvb3JkcyA9IE51bWVyaWMuemVyb3MoKHNpemUsMyksImQiKQpuYW1lcyA9IFtdCgpmb3Ig aSBpbiByYW5nZShzaXplKToKICAgIGxpbmUgPSBmaWxlLnJlYWRsaW5lKCkKICAgIGluZm8gPSBs aW5lLnNwbGl0KCkKICAgIGZvciBqIGluIHJhbmdlKDMpOgogICAgICAgIGF0b21jb29yZHNbaSxq XSA9IGZsb2F0KGluZm9baisxXSkKCiAgICBuYW1lcy5hcHBlbmQoaW5mb1swXSkKZmlsZS5jbG9z ZSgpCgptYXRyaXggPSBOdW1lcmljLmFycmF5KFtbY29zKGFuZ2xlKnBpLzE4MCksIHNpbihhbmds ZSpwaS8xODApLCAwXSwKICAgICAgICAgICAgICAgICAgICAgICAgWy0xKnNpbihhbmdsZSpwaS8x ODApLCBjb3MoYW5nbGUqcGkvMTgwKSwgMF0sCiAgICAgICAgICAgICAgICAgICAgICAgIFswLCAw LCAxXV0pCgpmb3IgaSBpbiByYW5nZShzaXplKToKIyAgICBpZiBhdG9tY29vcmRzW2ksMl0gPCAw OgojICAgICAgICBjb250aW51ZQoKICAgIHRlbXAgPSBOdW1lcmljLm1hdHJpeG11bHRpcGx5KGF0 b21jb29yZHNbaV0sIG1hdHJpeCkKICAgIGF0b21jb29yZHNbaV0gPSB0ZW1wCgpmaWxlID0gb3Bl bigicm90YXRlZC54eXoiLCJ3IikKZmlsZS53cml0ZSgiJWlcblxuIiVzaXplKQpmb3IgaSBpbiBy YW5nZShzaXplKToKICAgIGZpbGUud3JpdGUoIiUtMnMgJTEzLjVmICUxMy41ZiAlMTMuNWZcbiIg JSAobmFtZXNbaV0sIGF0b21jb29yZHNbaSwwXSwgYXRvbWNvb3Jkc1tpLDFdLCBcCiAgICAgICAg ICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgICAgIGF0b21jb29yZHNbaSwyXSkp CgpmaWxlLmNsb3NlKCkK ------=_Part_3658_611816.1201806040105-- From owner-chemistry@ccl.net Thu Jan 31 22:45:00 2008 From: "Negi, Surendra S. ssnegi^-^utmb.edu" To: CCL Subject: CCL: Freeware for protein-small molecule minimization Message-Id: <-36180-080131184346-4509-WrbFEJdcNKR4zhkWnAt2bw]|[server.ccl.net> X-Original-From: "Negi, Surendra S." Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 31 Jan 2008 16:58:30 -0600 MIME-Version: 1.0 Sent to CCL by: "Negi, Surendra S." [ssnegi*utmb.edu] Use Antechamber(alone) or with Chimera. -----Original Message----- > From: Manali Joshi manali%%adrik.bchs.uh.edu = [mailto:owner-chemistry|ccl.net] Sent: Thu 1/31/2008 3:02 PM To: Negi, Surendra S. Subject: CCL: Freeware for protein-small molecule minimization =20 Sent to CCL by: "Manali Joshi" [manali**adrik.bchs.uh.edu] Hi, I have a protein and a list of thousands of small molecules in the = appropriate binding orientation. I want to be able to perform energy = minimization of the binding site of the protein with each small molecule = (using semi-empirical or similar charges). I am looking for freeware that can automate this process. Any help will be greatly appreciated. Thanks Manali -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20Search Messages: http://www.ccl.net/htdig (login: ccl, Password: = search)http://www.ccl.net/spammers.txt