From chemistry-request@server.ccl.net Tue May 15 03:07:27 2001 Received: from aquila.cscs.ch ([148.187.130.150]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4F77QI02701 for ; Tue, 15 May 2001 03:07:27 -0400 Received: from cscs.ch (bogno [148.187.130.109]) by aquila.cscs.ch (Mail) with ESMTP id 4DE1A1A833 for ; Tue, 15 May 2001 09:07:27 +0200 (MET DST) Sender: redaelli@cscs.ch Message-ID: <3B00D5AD.6DBF332B@cscs.ch> Date: Tue, 15 May 2001 09:07:25 +0200 From: "Claudio Redaelli (CSCS)" Organization: Swiss Center for Scientific Computing - Via Cantonale, CH-6928 Manno (CH) X-Mailer: Mozilla 4.7 [en] (X11; I; SunOS 5.7 sun4u) X-Accept-Language: en, el MIME-Version: 1.0 To: chemistry@ccl.net Subject: CHARMM - MbCO Output Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLer's, I am looking for the results (output, not timing!) of the famous CHARMM test concerning MbCO and 3830 water molecules. Does anyone help me? Thanks in advance Claudio Redaelli -- Claudio Redaelli mailto:Claudio.Redaelli@cscs.ch HPC Applications Support Tel: +41(91)610 8241 Swiss Center for Scientific Computing Fax: +41(91)610 8282 Via Cantonale, CH-6928 Manno (CH) http://www.cscs.ch/~redaelli From chemistry-request@server.ccl.net Tue May 15 02:51:29 2001 Received: from nms.kyunghee.ac.kr ([163.180.16.53]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4F6pSI02525 for ; Tue, 15 May 2001 02:51:29 -0400 Received: from deutron (deutron.kyunghee.ac.kr [163.180.104.151]) by nms.kyunghee.ac.kr (8.9.3/8.9.3) with SMTP id PAA24041 for ; Tue, 15 May 2001 15:51:45 +0900 (KST) From: =?ks_c_5601-1987?B?sei+57z2?= To: Subject: How to compile g98 A.9 on redhat linux 7.1(kernel 2.4.2-2)? Date: Tue, 15 May 2001 15:54:15 +0900 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="ks_c_5601-1987" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id f4F6pTI02528 I tried to compile g98 A.9 on Coppermine Pentium III 650E under RedHat Linux 7.1 (Kernel 2.4.2-2). I used the PGF77 Compiler(15-day trial). I used blas libraries... So I downloaded blas-f2c.a at http://www.gaussian.com/g98_req.htm and blas-opt.a (renamed lsblasppro1.1o_08.99.a to blas-opt.a) at http://www.cs.utk.edu/~ghenry/distrib/. I modified the g98.make file such as below: # BLAS = blas.a BLAS = /usr/local/lib/blas-opt.a /usr/local/lib/blas-f2c.a MACH = -tp p6 # MACH = -tp p5 GAULIBA = util.a GAULIB = $(GAULIBA) $(BLAS) # GAULIB = util.so RUNF77 = pgf77 F2CLIB = LIBS = UNROLL = -Munroll VECTOR = -Mvect=cachesize:262144 But when it comes to compile ml0.F, I get an error. The error message is below: make -f bsd/g98.make JUNK1=JUNK exe gau-fsplit -e ml0 bsd/main.F ml0.F make -f bsd/g98.make OPTFLAG=' -O2 -tp p6 -Munroll -Mvect=cachesize:262144' ml0.o make[1]: Entering directory `/applic/g98' gau-cpp -I/applic/g98 -I/applic/g98s -DGAUSS_PAR -DGAUSS_THPAR -DDEFMAXSHL=20000 -DDEFMAXATM=20000 -DDEFMAXNZ=20000 -DDEFNVDIM=257 -DDEFARCREC=1024 -DMERGE_LOOPS -DUSE_ESSL -D_I386_ -DLITTLE_END -DUSING_F2C -DDEFMAXIOP=100 -DDEFMAXCHR=1024 -DDEFLMAX=13 -DDEFN3MIN=10 -DDEFMAXHEV=2000 -DDEFCACHE=64 -DDEFMAXLECP=10 -DDEFMAXFUNIT=5 -DDEFMAXFFILE=10000 -DDEFMAXFPS=1300 -DDEFMAXINFO=200 -DDEFMAXOP=120 -DDEFMAXTIT=100 -DDEFMAXRTE=4000 -DDEFMAXOV=500 -D_ALIGN_CORE_ -DCA1_DGEMM -DCA2_DGEMM -DCAB_DGEMM -DLV_DSP -DO_BKSPEF -DDEFMXTS=1500 -DDEFMXBAS=500 -DDEFMXOPT=50 -DDEFMXBOND=12 -DDEFMXSPH=250 -DDEFMXINV=1500 ml0.F ml0.f pgf77 -O2 -tp p6 -Munroll -Mvect=cachesize:262144 -c ml0.f NOTE: your evaluation license will expire in 14 days, 1.42 hours. rm -f ml0.f ml0.c make[1]: Leaving directory `/applic/g98' pgf77 -O2 -tp p6 -Munroll -Mvect=cachesize:262144 -o g98 ml0.o util.a /usr/local/lib/blas-opt.a /usr/local/lib/blas-f2c.a ml0.o: In function `MAIN_': ml0.o(.text+0x296): undefined reference to `gauabt_' ml0.o(.text+0x330): undefined reference to `gauabt_' ml0.o(.text+0x402): undefined reference to `gauabt_' ml0.o(.text+0x4dc): undefined reference to `gauabt_' ml0.o(.text+0x619): undefined reference to `gauabt_' ml0.o(.text+0x63c): undefined reference to `fixinout_' ml0.o(.text+0xe47): undefined reference to `ggeten_' ml0.o(.text+0xea8): undefined reference to `getexen_' ml0.o(.text+0x112c): undefined reference to `gsyst_' util.a(getscd.o): In function `getscd_': getscd.o(.text+0x10a): undefined reference to `ggeten_' util.a(lnk1e.o): In function `lnk1e_': lnk1e.o(.text+0x1f9): undefined reference to `gauabt_' util.a(prsarg.o): In function `prsarg_': prsarg.o(.text+0x2b7): undefined reference to `gauabt_' util.a(tstfil.o): In function `tstfil_': tstfil.o(.text+0x8bc): undefined reference to `envfil_' tstfil.o(.text+0x90c): undefined reference to `envfil_' util.a(chain.o): In function `chain_': chain.o(.text+0xcb2): undefined reference to `gauabt_' chain.o(.text+0xcb9): undefined reference to `gfree_' chain.o(.text+0xd14): undefined reference to `gauexec_' util.a(fioadd.o): In function `fioadd_': fioadd.o(.text+0x140): undefined reference to `imove_' util.a(fiodel.o): In function `fiodel_': fiodel.o(.text+0x27f): undefined reference to `imove_' fiodel.o(.text+0x2c2): undefined reference to `ibkmov_' fiodel.o(.text+0x2f9): undefined reference to `imove_' util.a(getatf.o): In function `getatf_': getatf.o(.text+0x222): undefined reference to `envfil_' util.a(ilsw.o): In function `ilsw_': ilsw.o(.text+0x556): undefined reference to `imove_' util.a(ntrclo.o): In function `ntrclo_': ntrclo.o(.text+0x2fd): undefined reference to `gfree1_' ntrclo.o(.text+0x313): undefined reference to `closwa_' util.a(ntrerr.o): In function `ntrerr_': ntrerr.o(.text+0x92): undefined reference to `gauabt_' util.a(ntrext.o): In function `ntrext_': ntrext.o(.text+0x289): undefined reference to `galloc1_' ntrext.o(.text+0x313): undefined reference to `ntrext1_' ntrext.o(.text+0x33d): undefined reference to `ntrsiz_' util.a(ntrio.o): In function `ntrio_': ntrio.o(.text+0x364): undefined reference to `imove_' ntrio.o(.text+0x3d3): undefined reference to `imove_' ntrio.o(.text+0x416): undefined reference to `writwa_' ntrio.o(.text+0x450): undefined reference to `readwa_' util.a(ntrwat.o): In function `ntrwat_': ntrwat.o(.text+0x7c): undefined reference to `waitwa_' util.a(ntstat.o): In function `ntstat_': ntstat.o(.text+0x313): undefined reference to `ntrbks_' util.a(fiocmp.o): In function `fiocmp_': fiocmp.o(.text+0x8e): undefined reference to `imove_' fiocmp.o(.text+0x164): undefined reference to `imove_' fiocmp.o(.text+0x1a8): undefined reference to `imove_' fiocmp.o(.text+0x1df): undefined reference to `imove_' util.a(ntropn.o): In function `ntropn_': ntropn.o(.text+0x394): undefined reference to `galloc1_' ntropn.o(.text+0x3f4): undefined reference to `openwa_' ntropn.o(.text+0x435): undefined reference to `openwa_' ntropn.o(.text+0x488): undefined reference to `openwa_' ntropn.o(.text+0x799): undefined reference to `ntrsiz_' make: *** [g98] Error 1 endif What is the problems? Please, Send me an e-mail how to compile g98 on Redhat 7.1. (in detail...) Have a nice day... Regards... Yangsoo Kim From chemistry-request@server.ccl.net Tue May 15 09:35:56 2001 Received: from smtp10.atl.mindspring.net ([207.69.200.246]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4FDZrI14595 for ; Tue, 15 May 2001 09:35:54 -0400 Received: from weasel.earthlink.net (user-vcauqb4.dsl.mindspring.com [216.175.105.100]) by smtp10.atl.mindspring.net (8.9.3/8.8.5) with ESMTP id JAA32044 for ; Tue, 15 May 2001 09:35:48 -0400 (EDT) Message-Id: <5.0.2.1.0.20010515063400.00b15908@mail.earthlink.net> X-Sender: greglandrum@mail.earthlink.net X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Tue, 15 May 2001 06:38:03 -0700 To: chemistry@ccl.net From: Greg Landrum Subject: Status of DeFT Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hi, Does anyone know what has become of Alain St-Amant's DeFT program? I've been trying what I believe is the official site for the program (http://www.chem.uottawa.ca/DeFT.html) for the past couple of weeks and it appears to be dead (www.chem.uottawa.ca is there with Apache's standard "you did it" page, but DeFT.html gives a 404). Thanks, -greg ---- greg Landrum (greglandrum@earthlink.net) Software Carpenter/Computational Chemist From chemistry-request@server.ccl.net Tue May 15 12:50:10 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4FGoAI15707 for ; Tue, 15 May 2001 12:50:10 -0400 Received: from mailhost.msi.com (fire.msi.com [146.202.0.242]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id MAA11309 for ; Tue, 15 May 2001 12:50:07 -0400 (EDT) Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id JAA12942 for ; Tue, 15 May 2001 09:49:49 -0700 (PDT) Received: from dial10.msi.com(146.202.9.110) by mailhost.msi.com via smap (V2.0) id xma012932; Tue, 15 May 01 09:49:31 -0700 Message-Id: <5.1.0.14.2.20010515094930.00af8ce0@146.202.6.130> X-Sender: dgregory@146.202.6.130 X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Tue, 15 May 2001 09:50:43 -0700 To: chemistry@ccl.net (Comp. Chem. List) From: Don Gregory Subject: Re: CCL:CHARMM - MbCO Output In-Reply-To: <3B00D5AD.6DBF332B@cscs.ch> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hi Claudio, There is a good deal of information about these CHARMM tests at Milan Hodoscek's web-site, specifically: http://kihp6.ki.si/parallel.html Hope this helps! Don Gregory At 5/15/2001 +0200, you wrote: >Dear CCLer's, > > I am looking for the results (output, not timing!) of the famous > CHARMM test concerning MbCO and 3830 water molecules. > Does anyone help me? > >Thanks in advance >Claudio Redaelli > >-- >Claudio Redaelli mailto:Claudio.Redaelli@cscs.ch >HPC Applications Support Tel: +41(91)610 8241 >Swiss Center for Scientific Computing Fax: +41(91)610 8282 >Via Cantonale, CH-6928 Manno (CH) http://www.cscs.ch/~redaelli > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Tue May 15 11:33:59 2001 Received: from alien.biochem.wfubmc.edu ([152.11.118.46]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4FFXwI15331 for ; Tue, 15 May 2001 11:33:59 -0400 Received: from alien.biochem.wfubmc.edu (localhost [127.0.0.1]) by alien.biochem.wfubmc.edu (SGI-8.9.3/8.9.3) with ESMTP id LAA64789; Tue, 15 May 2001 11:33:01 -0400 (EDT) Sender: zhangxd@alien.biochem.wfubmc.edu Message-ID: <3B014C2D.1D2FDC14@alien.biochem.wfubmc.edu> Date: Tue, 15 May 2001 11:33:01 -0400 From: Zhangxd X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: AMBER-LIST CC: chemistry@ccl.net Subject: the program and references References: <200105140743.f4E7hHc01023@protege.snu.ac.kr> <3AFFEA32.F0E0FCD8@structbio.vanderbilt.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit hi, everyone I want to know the methods and references of erengy miniization, MD and time-average, which are similar to these in AMBER, for comparsion the results. With best regards, sincerely yours, dong From chemistry-request@server.ccl.net Tue May 15 11:33:26 2001 Received: from mailhost.msi.com ([146.202.0.242]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4FFXPI15318 for ; Tue, 15 May 2001 11:33:26 -0400 Received: (from daemon@localhost) by mailhost.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id IAA05915 for ; Tue, 15 May 2001 08:33:36 -0700 (PDT) Received: from unknown(146.202.5.50) by mailhost.msi.com via smap (V2.0) id xmab05850; Tue, 15 May 01 08:33:03 -0700 Message-Id: <5.1.0.14.0.20010515082732.00a7c490@pop3.norton.antivirus> X-Sender: jnauss/sparky2.msi.com@pop3.norton.antivirus X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Tue, 15 May 2001 08:28:27 -0400 To: chemistry@ccl.net From: Jeff Nauss Subject: MSI InsightII Training Workshops in San Diego Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Molecular Simulations Inc. will be holding a pair of 2-day workshops at the San Diego Supercomputer Center, La Jolla, CA, in July. Both workshops will use the InsightII interface. On July 10-11, the workshop "Introduction to Life Science Modeling with InsightII" will be offered. This course provides an overview of molecular modeling techniques for life sciences applications in the InsightII graphical user environment. Prior modeling experience is not assumed making this course a great place to start molecular modeling. On July 12-13, the "Homology-Based Protein Design" training will be offered. This workshop is relevant to any of our customers who are interested in predicting protein structure and who would like to make more effective use of modeling in their work. During the two-day workshop, the process of producing a three-dimensional model from an amino acid sequence will be covered step-by-step. Both manual and automatic methodologies will be discussed. Prerequisites for this course are the "Introduction to Life Science Modeling with InsightII" workshop or extensive experience with InsightII. Fees for each 2-day course are $1000 commercial, $500 government, and $400 academic. However, register for both courses and receive a 25% discount for the second course. Please note that on June1, MSI, Synopsys, Oxford Molecular, and GCG will become Accelrys. Further detailed information about this and other MSI training workshops, as well as on-line course registration, can be found at MSI's website (http://www.msi.com/about/events/training). Please do not hesitate to contact us should you have any questions. Thank you very much. Jeffrey L. Nauss 858-799-5555 Chris Arzt 858-799-5340 -- Jeffrey L. Nauss, PhD Phone: (858) 799-5555 Customer Training Programs Fax: (858) 458-0136 Molecular Simulations Inc. E-mail: jnauss@msi.com 9685 Scranton Road http://www.msi.com/about/events/training San Diego, CA 92121-3752 MSI, Synopsys, Oxford Molecular, and GCG will become Accelrys on June 1 From chemistry-request@server.ccl.net Tue May 15 12:42:22 2001 Received: from pat.ccc.nottingham.ac.uk ([128.243.40.194]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f4FGgMI15655 for ; Tue, 15 May 2001 12:42:22 -0400 Received: from www.escalate.nottingham.ac.uk ([128.243.40.50] helo=gotham.ccc.nottingham.ac.uk) by pat.ccc.nottingham.ac.uk with esmtp (Exim 3.20 #2) id 14zhsf-00068K-00 for chemistry@ccl.net; Tue, 15 May 2001 17:41:05 +0100 Received: from granby ([128.243.40.43] helo=granby.ccc.nottingham.ac.uk) by gotham.ccc.nottingham.ac.uk with esmtp (Exim 3.20 #2) id 14zhtr-0001JR-00 for chemistry@ccl.net; Tue, 15 May 2001 17:42:19 +0100 Date: Tue, 15 May 2001 17:42:19 +0100 (BST) From: Simon Cross X-Sender: pcxsc@granby.ccc.nottingham.ac.uk To: ccl list Subject: Modelling software Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, some time ago I asked which software tools people liked to use and got a range of responses. I have compiled the replies below: ----------------------------------------- Simon Cross School of Chemistry University of Nottingham tel. 0115 9514193 Email: pcxsc@nottingham.ac.uk Date: Fri, 04 May 2001 17:06:10 +0100 From: Mark Forster To: Simon Cross Subject: Re: CCL:SYBYL Dear Simon We use a mixture (a) academic codes such as AMBER, Autodock etc, GAMESS. (b) Web based resources for sequence database searching, tools such as SwissModel for homology modelling. (c) Commercial tools such as insightII/Discover, Gaussian 98W. and choose the easist to use tool for the job. For interactive 3D model editing and other tasks the insightII tools are very comprehensive - hence it is hard to do without this completely. Mark Date: Fri, 4 May 2001 19:24:42 +0200 (CEST) From: Bernd Rupp To: Simon Cross Subject: Re: CCL:SYBYL Hi Simon, the usage of InsightII or Tripos depens from the problem you. I have no favoured packages. At this time i work at proteins so i work with insight. Other time, when i work with small molekules I prefer sybyl. here are some usefull sites whit a list of the most used programms: http://chpc06.ch.unito.it/chem_linux.html http://sal.kachinatech.com/index.shtml Tshoe Bernd -- Bernd Rupp Heinrich-Heine-Universitaet Duesseldorf | Gebaeude 26.23 Raum O2.33 Institut fuer Pharmazeutische Chemie | Tel.: 0211 / 81 - 1 38 27 Universitaetsstr. 1 | Fax.: 0211 / 81 - 1 38 47 40225 Duesseldorf | E-Mail: rupp@pharm.uni-duesseldorf.de Date: Fri, 04 May 2001 13:38:18 -0500 From: Abby Parrill To: Simon Cross Subject: Re: CCL:SYBYL Hi Simon, My group uses the following: MOE (Chemical Computing Group) Cerius2 (MSI) Amber6.0 (UCSF) Macromodel Gamess Dock/MidasPlus Autodock NACCESS MM3 SCORE > Hi, I would like to get an idea of the range of software that people > use for computational chemistry/drug design - do lots of people use > MSI software like InsightII or Tripos software like SYBYL or do most > academics use freeware of some kind? Are there any reviews that detail > advantages/disadvantages for these packages? We are using Macromodel from Schrodinger (www.schrodinger.com). For academic pricing, our experience is that Macromodel is a good bit cheaper than Insight (as stated on Schrodinger's web site, you can get a permanent network license for a 255-address subnet for Macromodel for $3k, and I seriously doubt MSI will discount the relevant modules of Insight down to anywhere near that level). > From a computational perspective, Macromodel is powerful. Its weakness is that it is not so good for visualization. For visualization, matters of cost aside, I much prefer Insight. I have not used SYBYL or dealt with Tripos. Another package that you might want to look at is ICM from Molsoft (www.molsoft.com). It runs on a ton of different platforms, and offers good visualization. However, in some respects it is not as computationally flexible as Macromodel (you are limited to MMFF, and one company rep I talked to couldn't tell me whether I could easily customize the force field). I don't think I've seen their pricing for the advanced modules of their program. -- Eric Bennett (ericb@pobox.com ; http://www.pobox.com/~ericb ) Overall description: packages, like SYBYL and Insight II have one great advantage : they have nice, more or less user friendly interface, so it is easier to start working with them. However, almost all the subprograms, included in those packages are available to academic users for free or really small fee, so there is the freeware solution: Modeller - homology modelling(free to academic institutions) Tinker - energy minimizations and dynamics freeware FT-dock, Autodock, Dock - docking programs (free to academic institutions) LigBuilder - Drug Design (free to academic institutions). And, of course, plenty of visualization programs. The disadvantage - command line and problems with the format conversions. So, the choice is on you Yours Sincerely RNDr. Bruno Sopko Dept. of Biochemistry, Charles University - Faculty of Science Albertov 2030 128 40 Praha 2, Czech Republic Phone: +420-2-21952173 Fax.: +420-2-21952331 Dear Simon, Good question. It is true that a lot of people are using InsightII, Cerius2, Quanta and SYBYL in the area of computational chemistry/drug design. These softwares usually provide a general interface, with which you can perform all the basic modeling, and many add-in modules, which are developed for more specific jobs, such as QSAR, docking, scoring, and so on. I think all of these softwares are acceptable for the general interface. You many want to have at least one of them. As for drug design, my personal choices are Sybyl and Cerius2. None of them is perfect though. For the specific "modules", the quality simply varies. Sometimes they are far from reliable. You must be very careful when you use them since the software company usually does not tell you that they may not work as well as what you have expected. There are a lot of academic programs in exsitence, which can out-perform those commercial softwares on a certain aspect. You may want to use some of them as enhancement or supplement in your work. Actually when an academic program becomes so successful, MSI or Tripos will probably purchase it and, after proper wrapping, put it into their all-in-one products. You can find a lot of such examples in the softwares I mentioned above. As one of the academic programmers, I would like to add some more comments: I will be glad to see that they (or we) work in an open, collaborating manner to develop a molecular modeling system of maximal common interests. Think about Linux and you know what I mean. All my best wishes, Renxiao Wang, Ph.D. Georgetown University Medical Center Dear Simon, take a look at www.chemcomp.com The Chemical Computing Group has developed a "next generation" modeling package. Besides covering the application areas High Throuput Discovery (with more than 300 QSAR descriptors built into MOE), focused library design, Homology Modeling and Structure based Design, it has the major advantages of being platform independent and coming with the source code. CCG has developed it's own programming language (SVL), that allows for a 10 to 1 reduction in lines of code. That makes it an ideal tool for both rapid software development and teaching. CCG gives MOE for free, if you use it for teaching! Please don't hesitate to contact me in case you have any further questions. Sincerely, Dr. Wolfram Altenhofen Director of Scientific Services Chemical Computing Group AG Wiesentalstr. 74a 79539 Lrrach Germany From: Malcolm Gillies My take on Sybyl vs Insight (based on not all too extensive use of either) is as follows: Insight has the edge in forcefields (though you have to pay extra for many of them); Insight seems better put together from a programmer's perspective, but less intuitive in terms of basic editing of chemical structures; Insight has more annoying bugs and quirks; Sybyl has more flexible tools for manipulating proteins and DNA; Insight has a more substantial MD code (Discover); Insight has better facilities for making publication quality ribbon diagrams etc; the Insight user interface is easier for beginners. Probably more important than any of these factors is the availability of special-purpose modules, and file-format compatibility with external programs. If you need to use FlexX, CHARMm, DelPhi etc, then your life will be much easier if you choose the program with the best compatibility. In the end, I used Insight more, and liked it less... cheers, Malcolm -- Malcolm Gillies Post-doctoral researcher Organic Chemistry, Dept of Chemistry, Technical University of Denmark From: Stephen Doughty To: pcxsc@nottingham.ac.uk Subject: Re: CCL:SYBYL Simon, Across in Phamaceutical Sciences we use a wealth of different software. Generally MSI and Tripos are the molecular modellers tools of choice. Each has its pros and cons, choices are usually made by what individual researchers cut their teeth on. Personally I think Sybyl is the best modelling software (I have that here), although it lacks some of the simple functionality of some MSI products (I prefered Quanta, but it is now pretty much unsupported; we have InsightII here at the moment). However, it more than makes up for it in terms of advanced functionality. However, the functionality you might want costs money. Free software - there's some good stuff out there now, VMD, WhatIf, NAMD, plus a few others. Again, it depends what you want to do - these are OK for modelling protein structures, but some are better at building than others (some don't include any building functionality at all). If you just want small molecule modelling, look at Spartan or Cache. If you want to do any proper modelling then you'll also need some molecular mechanics code - don't rely on the force fields given in the programs, for proteins you'll want either CHARMM or AMBER. Again, its horses of courses ... people (generaly) choose the software based on the type of modelling that they are likely to be doing. Let me know if you want more info or a more detailed discussion. Cheers, Stephen