From owner-chemistry@ccl.net Thu Dec 15 02:05:00 2005 From: "Marc Baaden baaden[#]smplinux.de" To: CCL Subject: CCL: Looking for Extended Huckel codes / ATP protonation state Message-Id: <-30324-051215020106-28802-03mAG6gF/d1xZLt3CHWgYQ() server.ccl.net> X-Original-From: "Marc Baaden" Sent to CCL by: "Marc Baaden" [baaden_._smplinux.de] Dear All, I am looking for a program or software package that allows to do extended Huckel calculations on charged molecules (nucleotides actually: ATP3-, ATP4-, ADP2-, ADP3- eventually in complex with Mg2+) and to visualize the calculated HOMO and LUMO. (I mention charged molecules, as I have some problems in doing this with the code I currently use) Ideally that code would run under Linux or Mac OSX, but I also have occasional access to Windows if that's the only solution. Furthermore I'd also appreciate any convincing piece of information about ATP/ADP's most likely protonation state in vivo. Thank you very much in advance, Marc Baaden -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baaden : smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 From owner-chemistry@ccl.net Thu Dec 15 06:21:00 2005 From: "Goedele Roos groos..vub.ac.be" To: CCL Subject: CCL: desolvatation energy Message-Id: <-30325-051215052227-4361-ZcJXfLJIodsT31ScfxtJEw(-)server.ccl.net> X-Original-From: Goedele Roos Date: Thu, 15 Dec 2005 11:22:15 +0100 (CET) Sent to CCL by: Goedele Roos [groos : vub.ac.be] Dear all, how can you calculate desolvatation energies? Or where can I find ones? I need the desolvatation ergy of Potassium and of sodium Thank you in advance, Best regards, Goedele Drs. Goedele Roos Dienst Algemene Chemie (ALGC) Vrije Universiteit Brussel (VUB) Pleinlaan 2 B-1050 Brussels Tel: 0032-2-629 35 16 Fax: 0032-2-629 33 17 From owner-chemistry@ccl.net Thu Dec 15 08:19:01 2005 From: "Szabolcs Csepregi szabolcs.csepregi .. chemaxon.hu" To: CCL Subject: CCL: Looking for Extended Huckel codes / ATP protonation state Message-Id: <-30326-051215081618-28082-EWczmJ5prg3hlF3oD9C7tg(-)server.ccl.net> X-Original-From: Szabolcs Csepregi Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 15 Dec 2005 13:20:50 +0100 MIME-Version: 1.0 Sent to CCL by: Szabolcs Csepregi [szabolcs.csepregi(~)chemaxon.hu] Marc, In connection to your second question I suggest to have a look at the Marvin plugins. (http://www.chemaxon.com/products.html#CalculatorPlugins) which are included in our packages (like Marvin Beans and JChem). The major microspecies plugin predicts the dominant protonation state at a specified pH. Furthermore, the pka plugin also provides a graph about the microspecies distribution. Example: http://www.chemaxon.com/marvin/chemaxon/marvin/help/calculator-plugins.html#pka Marvin's Calculator Plugins (as all ChemAxon products) are free for registered academic licensees: http://www.chemaxon.com/forum/ftopic193.html Now you can also run the predictions one-by-one online for free at our web site: http://www.chemaxon.com/marvin/doc/dev/example-sketch1.1.html For batch or off-line calculations I suggest to download Marvin Beans > from our web site. Best regards, Szabolcs --- +36 20 4219863, +36 24 444243 skype:szabolcs.csepregi From owner-chemistry@ccl.net Thu Dec 15 09:17:00 2005 From: "John McKelvey jmmckel|a|attglobal.net" To: CCL Subject: CCL: Looking for Extended Huckel codes / ATP protonation state Message-Id: <-30327-051215061455-6011-rgokCy6qk9nOzs6DEntUKg _ server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 15 Dec 2005 05:34:45 -0500 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel[A]attglobal.net] Try www.linux4chemistry.com for YAEHMOP [Yet Another Extended Huckel Molecular Orbital Program].. John McKelvey Marc Baaden baaden[#]smplinux.de wrote: >Sent to CCL by: "Marc Baaden" [baaden_._smplinux.de] >Dear All, > >I am looking for a program or software package that allows to do extended Huckel calculations on charged molecules (nucleotides actually: ATP3-, >ATP4-, ADP2-, ADP3- eventually in complex with Mg2+) and to visualize the >calculated HOMO and LUMO. (I mention charged molecules, as I have some >problems in doing this with the code I currently use) > >Ideally that code would run under Linux or Mac OSX, but I also have occasional access to Windows if that's the only solution. > >Furthermore I'd also appreciate any convincing piece of information about >ATP/ADP's most likely protonation state in vivo. > >Thank you very much in advance, >Marc Baaden > > From owner-chemistry@ccl.net Thu Dec 15 09:52:00 2005 From: "jean jean,+,science.uct.ac.za" To: CCL Subject: CCL: Compiling autodock on Windows Message-Id: <-30328-051215091313-15850-r2CBBB8Ehq66vRJ9O9nSow:-:server.ccl.net> X-Original-From: jean Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Thu, 15 Dec 2005 14:50:07 +0200 MIME-Version: 1.0 Sent to CCL by: jean [jean~~science.uct.ac.za] Dear all I would like to set up autodock to run on a Windows 98 PC. I'm not that experienced with compiling from source and was hoping that somewhere there was a "follow-these-easy-steps" list of what to do. I haven't been able to find one yet though, so was wondering if anyone on this mailing list could help? So far, I've installed Cygwin and been able to get addsol and atomtobnd working using cc. I've also found the autodock Makefile and edited it for Gnu/Linux (as per the instructions on the website) - but I get error messages when I try to Make. Does anyone have an idea what I'm doing wrong? Also, can one use AutodockTools on a Windows machine? Thanks in advance. Jean From owner-chemistry@ccl.net Thu Dec 15 10:27:00 2005 From: "Dipankar Roy dipankarroy#%#iitb.ac.in" To: CCL Subject: CCL: Looking for Extended Huckel codes / ATP protonation state Message-Id: <-30329-051215050804-29152-OsHDWYPaT7K5NBW8tpye6Q++server.ccl.net> X-Original-From: "Dipankar Roy" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 15 Dec 2005 14:18:38 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: "Dipankar Roy" [dipankarroy/./iitb.ac.in] Hi, Check in Prof. Roald Hoffman's web page for YAeHMOP. hope that may work. > Sent to CCL by: "Marc Baaden" [baaden_._smplinux.de] > Dear All, > > I am looking for a program or software package that allows to do extended > Huckel calculations on charged molecules (nucleotides actually: ATP3-, > ATP4-, ADP2-, ADP3- eventually in complex with Mg2+) and to visualize the > calculated HOMO and LUMO. (I mention charged molecules, as I have some > problems in doing this with the code I currently use) > > Ideally that code would run under Linux or Mac OSX, but I also have > occasional access to Windows if that's the only solution. > > Furthermore I'd also appreciate any convincing piece of information about > ATP/ADP's most likely protonation state in vivo. > > Thank you very much in advance, > Marc Baaden > -- > Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris > mailto:baaden]*[smplinux.de - http://www.baaden.ibpc.fr > FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217> > > > *********************************************** Dipankar Roy Graduate Student of Prof. R. B. Sunoj Computational Chemistry Laboratoty Dept. of Chemistry Indian Institute of Technology, Bombay India - 400076 Phone: +91-22-2576-4130(lab) *********************************************** If your life is free of any failure You are not taking risks for success From owner-chemistry@ccl.net Thu Dec 15 11:02:01 2005 From: "Aurelie Perrier perrier/./itodys.jussieu.fr" To: CCL Subject: CCL:G: g98 compilation on linux: looking for "blas-opt.a" library Message-Id: <-30330-051215085348-14253-NoAsCqW8t55DWgUTMe1OYg^^^server.ccl.net> X-Original-From: "Aurelie Perrier" Sent to CCL by: "Aurelie Perrier" [perrier|-|itodys.jussieu.fr] Dear all, I am trying to compile g98 on a PIV dual core under Suse 9.3 (Kernel 2.6.11.4-20) using the PGF77 compiler (15-day trial). To this purpose, I need "blas-opt.a" but I cannot find this library. Can someone help me? Thanks in advance, Best Regards, Aurelie Perrier From owner-chemistry@ccl.net Thu Dec 15 11:37:00 2005 From: "David F. Green dfgreen _ ams.sunysb.edu" To: CCL Subject: CCL: Looking for Extended Huckel codes / ATP protonation state Message-Id: <-30331-051215092534-27725-Q/x//ou3m1x3ye/A5+XEXQ-.-server.ccl.net> X-Original-From: "David F. Green" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 15 Dec 2005 09:23:11 -0500 MIME-Version: 1.0 Sent to CCL by: "David F. Green" [dfgreen,,ams.sunysb.edu] The protonation and ion binding constants of ATP and ADP are such that the transition between states is positioned right in the biologically relevant concentration range, making this an important, but a bit tricky issue. There is a lot of data on the question, though, so it's not hard to make an intelligent choice. I would suggest NOT using computation methods to try to predict the preferred states, when there has been so much good analytical chemistry done on exactly this question. When free in solution, I don't see any reason why the predominant states of ATP and ADP would be different in vivo than under the same ionic strength and pH conditions in vitro. For pKa's and ion binding constants, see: Sigel, IH. Eur. J. Biochem. 165: 65-72 (1987). Smith, RM; Martell, AE; Chen, Y. Pure & Appl. Chem. 63:1015-108 (1991). and at higher temperatures: Oscarson, JL et al. J. Sol. Chem. 24: 171-200 (1995). Wang, P, et al. J. Sol. Chem. 24: 989-1012 (1995). These are just a few references; this is a problem that has been studied a lot, so there is no lack of experimental data. The biggest question will likely be what the ion concentrations (both in contributing to ionic strength, and in directly contributing to the Mg binding equilibrium), and pH are in the particular location you are interested in. IIRC, for ATP, the most populated states in a "typical" intracellular environment are [ATP.Mg]2-, ATP4-, ATPH3-, (the pKa of the first protonation is around 6.5, and the Kd of Mg2+ dissociation is around 50 uM). For ADP, I believe that again the first pKa is ~6.5, but the Kd of ion dissociation is higher (maybe 10-fold or so?), so ADP3- and ADPH2- should be present in relatively increased amounts, but [ADP.Mg]- is likely a significantly populated species. Now, when bound to a protein, all bets are off, and almost any species could be predominant in the bound state. Many favour [ATP.Mg]2-, and others favour ATP4- or ATPH3-, but there are cases where other species, such as [ATP.3Mg]2+, are preferred. For bound state populations, analysis of the structure is a must, and often it is very clear what the preferred form will be. ======================================================================== David F. Green Assistant Professor http://www.ams.sunysb.edu/~dfgreen/ Applied Mathematics and Statistics Stony Brook University Office: +1-631-632-9344 Math Tower, Room 1-117 Mobile: +1-617-953-3922 Stony Brook, NY 11794-3600 Fax: +1-631-632-8490 ======================================================================== Marc Baaden baaden[#]smplinux.de wrote: > Sent to CCL by: "Marc Baaden" [baaden_._smplinux.de] > Dear All, > > I am looking for a program or software package that allows to do extended Huckel calculations on charged molecules (nucleotides actually: ATP3-, > ATP4-, ADP2-, ADP3- eventually in complex with Mg2+) and to visualize the > calculated HOMO and LUMO. (I mention charged molecules, as I have some > problems in doing this with the code I currently use) > > Ideally that code would run under Linux or Mac OSX, but I also have occasional access to Windows if that's the only solution. > > Furthermore I'd also appreciate any convincing piece of information about > ATP/ADP's most likely protonation state in vivo. > > Thank you very much in advance, > Marc Baaden From owner-chemistry@ccl.net Thu Dec 15 12:12:00 2005 From: "Vlad Cojocaru Vlad.Cojocaru++eml-r.villa-bosch.de" To: CCL Subject: CCL: convergence of optimization for heme Fe3+ Message-Id: <-30332-051215094601-4562-UEaGaJYmKI9SXV2nEY47Bg ~~ server.ccl.net> X-Original-From: Vlad Cojocaru Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 15 Dec 2005 15:45:21 +0100 MIME-Version: 1.0 Sent to CCL by: Vlad Cojocaru [Vlad.Cojocaru * eml-r.villa-bosch.de] Dear CCLers, I have been trying to optimize the geometry of a heme group that has Fe3+ (both in low and high spin states - mult=2, mult=6). For this purpose I use GAMESS with the input shown below. However, the convergence is not achieved and the energy fluctuates widely (as shown in the output sample below). I am not an expert in QM calculations, so I was wondering if somebody could give me a hint how to deal with this or let me know if my input needs to be changed in any way? The result is very similar for MULT=2. Best wishes vlad GAMESS input: $CONTRL ICHARG=-2 MULT=2 RUNTYP=OPTIMIZE SCFTYP=UHF MAXIT=200 COORD=ZMT $END $SCF CONV=1.0E-06 FDIFF=.F. DIRSCF=.TRUE. $END $SYSTEM TIMLIM=50000 MWORDS=8 MEMDDI=0 $END $STATPT NSTEP=2000 OPTTOL=1.0E-04 $END $BASIS GBASIS=N31 NGAUSS=6 $END $GUESS GUESS=HUCKEL $END $DATA .... $END Output sample: --------------------------- UHF SCF CALCULATION --------------------------- NUCLEAR ENERGY = 7383.8785347619 MAXIT =200 NPUNCH= 2 MULT= 6 EXTRAP=T DAMP=F SHIFT=F RSTRCT=F DIIS=T SOSCF=F DENSITY MATRIX CONV= 2.00E-06 MEMORY REQUIRED FOR UHF/ROHF STEP= 2964074 WORDS. DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=F SCHWARZ INEQUALITY OVERHEAD: 98533 INTEGRALS, T= 0.15 NONZERO BLOCKS ITER EX TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS ERROR INTEGRALS SKIPPED 1 0 -3720.2759873169 -3720.2759873169 1.713419565 0.570028651 1300325523 268250525 2 1 -3707.8437086668 12.4322786501 38.445745834 0.595792411 1303138308 268005378 3 2 -3056.1712069807 651.6725016862 363.157129458 1.135176775 1305230198 265909997 4 3 -1788.6092030070 1267.5620039737 362.989932254 2.937931571 1310651084 262356372 5 4 613.7315607561 2402.3407637631 825.440015998 1.037018505 1306900567 262781564 6 5 -141.8318777457 -755.5634385018 825.626187912 8.537156278 1309087885 261949456 7 0 987.9107844740 1129.7426622197 390.659726349 1.021834652 1306164451 262904140 8 1 -2660.9936665301 -3648.9044510041 192.364998167 1.135433799 1309966646 264097527 9 2 -1525.2428607747 1135.7508057554 594.259290059 1.749986406 1306803145 263465700 10 3 -1195.0720412904 330.1708194843 596.124265744 3.206412328 1311607287 261814882 11 4 -252.6029086337 942.4691326568 714.714410041 1.004869464 1305259124 263194168 12 5 -677.9312536606 -425.3283450269 715.167434939 7.610254327 1310914762 261865307 13 6 347.0325994336 1024.9638530942 804.339857143 1.046661781 1303864371 263215751 14 7 -257.0557181790 -604.0883176126 804.367026727 9.378612013 1309920476 261763797 15 8 566.4361275300 823.4918457089 803.640561977 1.047754590 1305371645 263088084 16 9 -88.7210373938 -655.1571649237 803.638083407 6.807345138 1308982020 262090743 17 0 838.3569803008 927.0780176946 448.176130897 1.042140335 1306175723 263015441 18 1 -2249.0486510023 -3087.4056313031 351.965369776 1.135429772 1307145886 264285035 19 2 -1192.4104767561 1056.6381742462 709.278399327 1.668127022 1302844619 263969979 -- Dr. Vlad Cojocaru EML Research gGmbH Molecular and Cellular Modeling Group Villa Bosch Schloss-Wolfsbrunnenweg 33 69118 Heidelberg Germany Phone: +49-6221-533266 Fax: +49-6221-533298 e-mail: Vlad.Cojocaru-$-eml-r.villa-bosch.de Additional info: my home page From owner-chemistry@ccl.net Thu Dec 15 12:47:01 2005 From: "David F. Green dfgreen_-_ams.sunysb.edu" To: CCL Subject: CCL: desolvatation energy Message-Id: <-30333-051215095250-6372-jDoL6u4JXUPbRQxHQPLubw:-:server.ccl.net> X-Original-From: "David F. Green" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 15 Dec 2005 09:50:27 -0500 MIME-Version: 1.0 Sent to CCL by: "David F. Green" [dfgreen : ams.sunysb.edu] Among dozens of other sources: Thermodynamics of Solvation of Ions: Part 5. Gibbs Free Energy of Hydration at 298.15K Marcus, Y. J. Chem. Soc. Faraday Trans. 87: 2995-2999 (1991). Honestly, data like this should be very easy to find with a simple literature search. ======================================================================== David F. Green Assistant Professor http://www.ams.sunysb.edu/~dfgreen/ Applied Mathematics and Statistics Stony Brook University Office: +1-631-632-9344 Math Tower, Room 1-117 Mobile: +1-617-953-3922 Stony Brook, NY 11794-3600 Fax: +1-631-632-8490 ======================================================================== Goedele Roos groos..vub.ac.be wrote: > Sent to CCL by: Goedele Roos [groos : vub.ac.be] > Dear all, > how can you calculate desolvatation energies? Or where can I find ones? I need the desolvatation ergy of Potassium and of sodium > Thank you in advance, > Best regards, Goedele > > > Drs. Goedele Roos > Dienst Algemene Chemie (ALGC) > Vrije Universiteit Brussel (VUB) > Pleinlaan 2 > B-1050 Brussels > Tel: 0032-2-629 35 16 > Fax: 0032-2-629 33 17> > > From owner-chemistry@ccl.net Thu Dec 15 13:22:00 2005 From: "Nuno A. G. Bandeira nuno.bandeira[a]ist.utl.pt" To: CCL Subject: CCL: Looking for Extended Huckel codes / ATP protonation state Message-Id: <-30334-051215095836-10843-Dg3LNOHK+IFLRCrSp3G7HQ[A]server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Thu, 15 Dec 2005 14:21:11 +0000 Mime-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira a ist.utl.pt] There's YAEHMOP for linux (look it up in sourceforge) and CACAO98 and SAMOA (from primecolor software) for Windows. -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student {=} IST,Lisbon -- -- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.1.371 / Virus Database: 267.13.13/200 - Release Date: 14-12-2005 From owner-chemistry@ccl.net Thu Dec 15 13:57:00 2005 From: "Andrew D. Fant fant{=}pobox.com" To: CCL Subject: CCL: Looking for Extended Huckel codes / ATP protonation state Message-Id: <-30335-051215101102-18628-bvUGZXQ54wNX6W7bCBH09w:+:server.ccl.net> X-Original-From: "Andrew D. Fant" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 15 Dec 2005 10:10:37 -0500 MIME-Version: 1.0 Sent to CCL by: "Andrew D. Fant" [fant]_[pobox.com] John McKelvey jmmckel|a|attglobal.net wrote: > Sent to CCL by: John McKelvey [jmmckel[A]attglobal.net] > Try www.linux4chemistry.com for YAEHMOP [Yet Another Extended Huckel > Molecular Orbital Program].. linux4chemistry.com appears to be defunct. The good news is that YAeHMOP is a sourceforge project and can be found at http://yaehmop.sourceforge.net/ . Happy Holidays, Andy -- Andrew Fant | And when the night is cloudy | This space to let Molecular Geek | There is still a light |---------------------- fant[a]pobox.com | That shines on me | Disclaimer: I don't Boston, MA | Shine until tomorrow, Let it be | even speak for myself From owner-chemistry@ccl.net Thu Dec 15 14:32:00 2005 From: "Faisal Rahman s101alif^mail.chem.itb.ac.id" To: CCL Subject: CCL:G: How to calculate Message-Id: <-30336-051215101731-19909-OU6+T8VEIngwDqfRLHqsUA^^^server.ccl.net> X-Original-From: "Faisal Rahman" Sent to CCL by: "Faisal Rahman" [s101alif=mail.chem.itb.ac.id] Dear all Hello I'am Faisal I'am doing my final project about transfer proton in hydrogen bonding between nucleobases and hydrogen chloride using Gaussian. Now I have problem in calculating the acidity of hydrogen chloride using gaussian. Could anyone tell me how to calculate the acidity of molecule in my case the acidity of hydrogen chloride. I'll very appreciate your help Thank's before. From owner-chemistry@ccl.net Thu Dec 15 15:07:00 2005 From: "Praveen shrivastava praveenshrivastav|,|yahoo.com" To: CCL Subject: CCL: Is there any book/review/web to learn QSAR/QSAR-3D from the basis? Message-Id: <-30337-051215101717-19738-9NwgrM30ql1TaCwCoLOVlQ%%server.ccl.net> X-Original-From: Praveen shrivastava Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-141039370-1134656220=:26633" Date: Thu, 15 Dec 2005 06:17:00 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Praveen shrivastava [praveenshrivastav#%#yahoo.com] --0-141039370-1134656220=:26633 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Dr Carlos Lagos A Thanks for your information Please let me know the free web based information for above papers thanks Praveen "Carlos Lagos A. carlos+/-cgb.cl" wrote: Sent to CCL by: "Carlos Lagos A." [carlos:_:cgb.cl] I suggest you this 2 papers from Kubinyi QSAR and 3D QSAR in drug design Part 1: methodology Drug Discovery Today, Volume 2, Issue 11, November 1997, Pages 457-467 And QSAR and 3D QSAR in drug design Part 2: applications and problems Drug Discovery Today, Volume 2, Issue 12, December 1997, Pages 538-546 Carlos Lagos A. Centro de Genómica y Bioinformática CGB http://www.cgb.cl D.BIO- Gerard Pujadas gerard.pujadas(a)urv.net wrote: > Sent to CCL by: "D.BIO- Gerard Pujadas" [gerard.pujadas]^[urv.net] > > Dear CCL list members, > > I would appreciate if you could point me to a > book, review, etc. where I could learn > QSAR/3D-QSAR from the basis. > > With many thanks in advances for your help > > Yours sincerely > > Gerardhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- Yahoo! Shopping Find Great Deals on Holiday Gifts at Yahoo! Shopping --0-141039370-1134656220=:26633 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Dear Dr Carlos Lagos A
Thanks for your information Please let me know the  free web based information for above papers
thanks
Praveen


"Carlos Lagos A. carlos+/-cgb.cl" <owner-chemistry]~[ccl.net> wrote:
Sent to CCL by: "Carlos Lagos A." [carlos:_:cgb.cl]
I suggest you this 2 papers from Kubinyi

QSAR and 3D QSAR in drug design Part 1: methodology
Drug Discovery Today, Volume 2, Issue 11, November 1997, Pages 457-467

And
QSAR and 3D QSAR in drug design Part 2: applications and problems
Drug Discovery Today, Volume 2, Issue 12, December 1997, Pages 538-546


Carlos Lagos A.
Centro de Genómica y Bioinformática CGB
http://www.cgb.cl




D.BIO- Gerard Pujadas gerard.pujadas(a)urv.net wrote:
> Sent to CCL by: "D.BIO- Gerard Pujadas" [gerard.pujadas]^[urv.net]
>
> Dear CCL list members,
>
> I would appreciate if you could point me to a
> book, review, etc. where I could learn
> QSAR/3D-QSAR from the basis.
>
> With many thanks in advances for your help
>
> Yours sincerely
>
> Gerardhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

http://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/chemistry/sub_unsub.shtml
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Find Great Deals on Holiday Gifts at Yahoo! Shopping --0-141039370-1134656220=:26633-- From owner-chemistry@ccl.net Thu Dec 15 17:13:00 2005 From: "Aniko Simon aniko|*|simbiosys.ca" To: CCL Subject: CCL: announcing eHiTS: Flexible ligand docking tool version 5.3 was released Message-Id: <-30338-051215155110-23977-7dTr0ypoI29Ksm/XxS3uXg()server.ccl.net> X-Original-From: Aniko Simon Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 15 Dec 2005 15:15:13 -0500 MIME-Version: 1.0 Sent to CCL by: Aniko Simon [aniko###simbiosys.ca] A new version of the flexible ligand docking tool eHiTS v5.3 was released today! At SimBioSys Inc. we are pleased to announce the release of the latest version of our flexible ligand docking tool, eHiTS 5.3. eHiTS 5.3 is a truly systematic and exhaustive docking tool that performs docking with no seed bias, automatically detects binding sites and evaluates all possible protonation states of the ligand and receptor in a single run. eHiTS 5.3 has a completely new approach to the scoring function problem. eHiTS 5.3 uses the temperature factors included in PDB files to create a set of "statistically derived empirical scoring functions". The result is a far more accurate docking algorithm, average results show a 25-30% improvement in the top scoring pose in terms of RMSD to the x-ray pose. The new scoring function can be easily trained or tuned using any available data to achieve even better results. eHiTS 5.3 also includes a very fast pre-screening filter tool that can screen 6 ligands per second on a single CPU PC, making it applicable for large ligand screens. To read more about what's new in eHiTS v5.3, please visit: http://www.simbiosys.ca/ehits/ehits_newfeatures.html For academic users: eHiTS 5.3 continues to be free to academic users, please fill in a demo request to obtain a free academic copy. For more information and to obtain an evaluation copy please visit www.simbiosys.ca Best wishes and have a good Holiday Season! Aniko -- Aniko Simon, PhD VP of Business Development SimBioSys Inc. From owner-chemistry@ccl.net Thu Dec 15 20:10:00 2005 From: "Sanyasi Sitha sitha+/-bc.edu" To: CCL Subject: CCL: Nucleic Acid--GROMACS Message-Id: <-30339-051215180047-23018-fV4R8CxEwlVrfle3iJseDw*_*server.ccl.net> X-Original-From: "Sanyasi Sitha" Sent to CCL by: "Sanyasi Sitha" [sitha_-_bc.edu] Hi I am trying to run brownian simmulations on an RNA molecule using GROMACS. To generate the .top and .gro files I used the the pdb2gmx of GROMACS. But I am not getting the required input files (.top & .gro) for my calculations (though I have now inclued the AMBER force field parmeter needed to do nucleic acid simmulation in GROMACS---http://folding.stanford.edu/ffamber/). Any help will be appreciated. Thanking you bye sanyasi sitha Boston College sitha]_[bc.edu From owner-chemistry@ccl.net Thu Dec 15 20:45:00 2005 From: "sudipta kumar sinha sudiptakumar_sinha|,|yahoo.com" To: CCL Subject: CCL: Force feild of cyclic oligosaccharides Message-Id: <-30340-051215151711-13512-Nhfj0TOPKwmJ37usGVcJzQ]=[server.ccl.net> X-Original-From: sudipta kumar sinha Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-491515816-1134674228=:89029" Date: Thu, 15 Dec 2005 11:17:08 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: sudipta kumar sinha [sudiptakumar_sinha#,#yahoo.com] --0-491515816-1134674228=:89029 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi everyone , I am sudipta an M.sc. student at IIT-KGP, I am doing my final year project about the dynamics of different non polar solvent around a cyclic oligosaccharides. Could anyone help me to know, how i get the force field of different cyclic oligosaccharides. I will appreaciate your kind help...... sudipta........ --------------------------------- Yahoo! Shopping Find Great Deals on Holiday Gifts at Yahoo! Shopping --0-491515816-1134674228=:89029 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
 Hi everyone ,
 
 I am sudipta an M.sc. student at IIT-KGP, I am doing my final year project about the dynamics of different non polar solvent around a cyclic oligosaccharides. Could anyone help me to know, how i get the force field of  different  cyclic oligosaccharides. I will appreaciate your kind help......

sudipta........

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Find Great Deals on Holiday Gifts at Yahoo! Shopping --0-491515816-1134674228=:89029-- From owner-chemistry@ccl.net Thu Dec 15 23:32:01 2005 From: "Brian Salter-Duke b_duke**octa4.net.au" To: CCL Subject: CCL: convergence of optimization for heme Fe3+ Message-Id: <-30341-051215220942-6788-Sb8bIi8DConmtoF9iFW6cQ-.-server.ccl.net> X-Original-From: Brian Salter-Duke Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Fri, 16 Dec 2005 10:07:02 +1100 Mime-Version: 1.0 Sent to CCL by: Brian Salter-Duke [b_duke/a\octa4.net.au] On Thu, Dec 15, 2005 at 12:17:56PM -0500, Vlad Cojocaru Vlad.Cojocaru++eml-r.villa-bosch.de wrote: > Sent to CCL by: Vlad Cojocaru [Vlad.Cojocaru * eml-r.villa-bosch.de] > Dear CCLers, > I have been trying to optimize the geometry of a heme group that has > Fe3+ (both in low and high spin states - mult=2, mult=6). For this > purpose I use GAMESS with the input shown below. However, the > convergence is not achieved and the energy fluctuates widely (as shown > in the output sample below). I am not an expert in QM calculations, so I > was wondering if somebody could give me a hint how to deal with this or > let me know if my input needs to be changed in any way? First, never do RUNTYP=OPTIMIZE until you have a converged single point. Then use the converged $VEC to get started on optimizing. Second, make sure you have the orbitals in the HUCKEL guess that you want and then use VSIFTing to ensure that they stay that way, You may have HOMO-LUMO swapping here. It is quite common for Fe compounds. Third, look at the $SCF section in the manual and try various other convergence options. You are using DIIS by default. Some of the others may be better here. Good luck, Brian. > The result is very similar for MULT=2. > > Best wishes > vlad > > GAMESS input: > > $CONTRL ICHARG=-2 MULT=2 RUNTYP=OPTIMIZE SCFTYP=UHF MAXIT=200 COORD=ZMT > $END > $SCF CONV=1.0E-06 FDIFF=.F. DIRSCF=.TRUE. $END > $SYSTEM TIMLIM=50000 MWORDS=8 MEMDDI=0 $END > $STATPT NSTEP=2000 OPTTOL=1.0E-04 $END > $BASIS GBASIS=N31 NGAUSS=6 $END > $GUESS GUESS=HUCKEL $END > $DATA > ... > $END > > > Output sample: > > > --------------------------- > UHF SCF CALCULATION > --------------------------- > > NUCLEAR ENERGY = 7383.8785347619 > MAXIT =200 NPUNCH= 2 MULT= 6 > EXTRAP=T DAMP=F SHIFT=F RSTRCT=F DIIS=T SOSCF=F > DENSITY MATRIX CONV= 2.00E-06 > MEMORY REQUIRED FOR UHF/ROHF STEP= 2964074 WORDS. > > DIRECT SCF CALCULATION, SCHWRZ=T FDIFF=F > SCHWARZ INEQUALITY OVERHEAD: 98533 INTEGRALS, T= 0.15 > > > NONZERO BLOCKS > ITER EX TOTAL ENERGY E CHANGE DENSITY CHANGE DIIS > ERROR INTEGRALS SKIPPED > 1 0 -3720.2759873169 -3720.2759873169 1.713419565 > 0.570028651 1300325523 268250525 > 2 1 -3707.8437086668 12.4322786501 38.445745834 > 0.595792411 1303138308 268005378 > 3 2 -3056.1712069807 651.6725016862 363.157129458 > 1.135176775 1305230198 265909997 > 4 3 -1788.6092030070 1267.5620039737 362.989932254 > 2.937931571 1310651084 262356372 > 5 4 613.7315607561 2402.3407637631 825.440015998 > 1.037018505 1306900567 262781564 > 6 5 -141.8318777457 -755.5634385018 825.626187912 > 8.537156278 1309087885 261949456 > 7 0 987.9107844740 1129.7426622197 390.659726349 > 1.021834652 1306164451 262904140 > 8 1 -2660.9936665301 -3648.9044510041 192.364998167 > 1.135433799 1309966646 264097527 > 9 2 -1525.2428607747 1135.7508057554 594.259290059 > 1.749986406 1306803145 263465700 > 10 3 -1195.0720412904 330.1708194843 596.124265744 > 3.206412328 1311607287 261814882 > 11 4 -252.6029086337 942.4691326568 714.714410041 > 1.004869464 1305259124 263194168 > 12 5 -677.9312536606 -425.3283450269 715.167434939 > 7.610254327 1310914762 261865307 > 13 6 347.0325994336 1024.9638530942 804.339857143 > 1.046661781 1303864371 263215751 > 14 7 -257.0557181790 -604.0883176126 804.367026727 > 9.378612013 1309920476 261763797 > 15 8 566.4361275300 823.4918457089 803.640561977 > 1.047754590 1305371645 263088084 > 16 9 -88.7210373938 -655.1571649237 803.638083407 > 6.807345138 1308982020 262090743 > 17 0 838.3569803008 927.0780176946 448.176130897 > 1.042140335 1306175723 263015441 > 18 1 -2249.0486510023 -3087.4056313031 351.965369776 > 1.135429772 1307145886 264285035 > 19 2 -1192.4104767561 1056.6381742462 709.278399327 > 1.668127022 1302844619 263969979 > > > -- > > > Dr. Vlad Cojocaru > EML Research gGmbH > Molecular and Cellular Modeling Group > Villa Bosch > Schloss-Wolfsbrunnenweg 33 > 69118 Heidelberg > Germany > Phone: +49-6221-533266 > Fax: +49-6221-533298 > e-mail: Vlad.Cojocaru^^eml-r.villa-bosch.de > > Additional info: my home page > > > -- Brian Salter-Duke (Brian Duke) b_duke^^octa4.net.au Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ.