From chemistry-request@server.ccl.net Mon Mar 12 05:14:24 2001 Received: from mail1.rrz.Uni-Koeln.DE (mail1.rrz.Uni-Koeln.DE [134.95.100.208]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2CAENw07476 for ; Mon, 12 Mar 2001 05:14:24 -0500 Received: from campfire.rrz.Uni-Koeln.DE (IDENT:39358@campfire.rrz.Uni-Koeln.DE [134.95.19.27]) by mail1.rrz.Uni-Koeln.DE (8.9.3/8.9.3) with ESMTP id LAA17471 for ; Mon, 12 Mar 2001 11:14:23 +0100 (MET) Received: (from a0580@localhost) by campfire.rrz.Uni-Koeln.DE (8.9.1a/8.9.1) id LAA01631 for chemistry@ccl.net; Mon, 12 Mar 2001 11:14:20 +0100 (MET) Date: Mon, 12 Mar 2001 11:14:20 +0100 From: Lars Packschies To: chemistry@ccl.net Subject: Redhat/G98/PGI - Error Message-ID: <20010312111419.E19987@campfire.rrz.Uni-Koeln.DE> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="UlVJffcvxoiEqYs2" Content-Disposition: inline User-Agent: Mutt/1.2.5i --UlVJffcvxoiEqYs2 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Dear CCLers, I'm trying to compile g98.A7 on a Redhat 7.0 (ok, not the best choice). PGF77 ist working fine (as far I coud see). But when it comes to build/link l402, I get an error. The text is attached. Is this a RH7-specific problem which means to install a different distribution ? It wouldn't surprise me anayway... Is anybody out there who compiled g98.A7 on a RH7 PIII-box ? Thanks in advance, Lars -- ,H + Dr. Lars Packschies ZAIK/RRZK, Robert-Koch-Str.10 + H H O | Chemistry Dpt. Support D-50931 Cologne | `O-H. | ,' `H | Comp.Dpt., Univ. of Cologne Phn (+49)221-478-7022 | `O-H + Packschies@rrz.uni-koeln.de Fax (+49)221-478-5568 + --UlVJffcvxoiEqYs2 Content-Type: text/plain; charset=us-ascii Content-Disposition: attachment; filename="g98error.log" [hopefully relevant] make -f bsd/g98.make OPTFLAG=' -O2 -tp p6 -Munroll -Mvect=cachesize:524288' l402.a ml402.o make[1]: Entering directory `/scratch/software/g98' make[1]: `l402.a' is up to date. gau-cpp -I/scratch/software/g98 -I/scratch/software/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 ml402.F ml402.f pgf77 -O2 -tp p6 -Munroll -Mvect=cachesize:524288 -c ml402.f rm -f ml402.f ml402.c make[1]: Leaving directory `/scratch/software/g98' ar x l402.a bd0402.o pgf77 -O2 -tp p6 -Munroll -Mvect=cachesize:524288 -o l402.exe ml402.o l402.a bd0402.o util.so bd0402.o: In function `bd0402_': bd0402.o(.text+0x0): multiple definition of `bd0402_' l402.a(bd0402.o)(.text+0x0): first defined here bd0402.o(.data+0x0): multiple definition of `expon3_' l402.a(bd0402.o)(.data+0x0): first defined here bd0402.o(.data+0x120): multiple definition of `alpha3_' l402.a(bd0402.o)(.data+0x120): first defined here bd0402.o(.data+0x5e8): multiple definition of `beta3_' l402.a(bd0402.o)(.data+0x5e8): first defined here bd0402.o(.data+0xab0): multiple definition of `atomi3_' l402.a(bd0402.o)(.data+0xab0): first defined here bd0402.o(.data+0xbd0): multiple definition of `twoel3_' l402.a(bd0402.o)(.data+0xbd0): first defined here bd0402.o(.data+0xf28): multiple definition of `onele3_' l402.a(bd0402.o)(.data+0xf28): first defined here bd0402.o(.data+0x1048): multiple definition of `refs_' l402.a(bd0402.o)(.data+0x1048): first defined here bd0402.o(.data+0x9608): multiple definition of `alptm_' l402.a(bd0402.o)(.data+0x9608): first defined here bd0402.o(.data+0x97e8): multiple definition of `pm3_' l402.a(bd0402.o)(.data+0x97e8): first defined here bd0402.o(.data+0xe178): multiple definition of `mndo_' l402.a(bd0402.o)(.data+0xe178): first defined here bd0402.o(.data+0x12b08): multiple definition of `ideap_' l402.a(bd0402.o)(.data+0x12b08): first defined here bd0402.o(.data+0x18f58): multiple definition of `ideas_' l402.a(bd0402.o)(.data+0x18f58): first defined here bd0402.o(.data+0x1f3a8): multiple definition of `istope_' l402.a(bd0402.o)(.data+0x1f3a8): first defined here bd0402.o(.data+0x1f700): multiple definition of `vsips_' l402.a(bd0402.o)(.data+0x1f700): first defined here bd0402.o(.data+0x20108): multiple definition of `atomic_' l402.a(bd0402.o)(.data+0x20108): first defined here bd0402.o(.data+0x207b8): multiple definition of `twoele_' l402.a(bd0402.o)(.data+0x207b8): first defined here bd0402.o(.data+0x22278): multiple definition of `betas_' l402.a(bd0402.o)(.data+0x22278): first defined here bd0402.o(.data+0x22c80): multiple definition of `onelec_' l402.a(bd0402.o)(.data+0x22c80): first defined here bd0402.o(.data+0x23688): multiple definition of `expont_' l402.a(bd0402.o)(.data+0x23688): first defined here bd0402.o(.data+0x24090): multiple definition of `multip_' l402.a(bd0402.o)(.data+0x24090): first defined here bd0402.o(.data+0x25148): multiple definition of `core_' l402.a(bd0402.o)(.data+0x25148): first defined here bd0402.o(.data+0x254a0): multiple definition of `alpha_' l402.a(bd0402.o)(.data+0x254a0): first defined here bd0402.o(.data+0x257f8): multiple definition of `elemts_' l402.a(bd0402.o)(.data+0x257f8): first defined here bd0402.o(.data+0x258d0): multiple definition of `natorb_' l402.a(bd0402.o)(.data+0x258d0): first defined here util.so: the use of `tmpnam' is dangerous, better use `mkstemp' /usr/pgi/linux86/lib/libpgftnrtl.a(cnfg.o): In function `__fio_scratch_name': cnfg.o(.text+0x33): the use of `tempnam' is dangerous, better use `mkstemp' make: *** [l402.exe] Error 1 endif --UlVJffcvxoiEqYs2-- From chemistry-request@server.ccl.net Mon Mar 12 10:40:21 2001 Received: from vytautas.vdu.lt (mail@vytautas.vdu.lt [193.219.38.33]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2CFYRw09459 for ; Mon, 12 Mar 2001 10:35:15 -0500 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp for chemistry@ccl.net id 14cTyZ-0005ql-00; Mon, 12 Mar 2001 17:11:11 +0200 Received: from vaidila.vdu.lt (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id RAA15283 for ; Mon, 12 Mar 2001 17:11:12 +0200 (GMT) Message-ID: <3AAC4C86.AE8E54BE@vaidila.vdu.lt> Date: Mon, 12 Mar 2001 05:11:51 +0100 From: "art'" X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: CCL: dibenzodioxin synthesis Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Hi, CCL'ers, Could anyone point me to the reference on methodology of dibenzodioxin synthesis. Thank you. A.Ziemys From chemistry-request@server.ccl.net Mon Mar 12 14:10:59 2001 Received: from mail.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2CJAxw10357 for ; Mon, 12 Mar 2001 14:10:59 -0500 Received: from mail.chem.tamu.edu ([165.91.177.32]) by mail.chem.tamu.edu (Post.Office MTA v3.5.3 release 223 ID# 0-64333U1000L100S0V35) with ESMTP id edu for ; Mon, 12 Mar 2001 13:11:24 -0600 Sender: yubo@ccl.net Message-ID: <3AAD1FDD.47D29DD9@mail.chem.tamu.edu> Date: Mon, 12 Mar 2001 19:13:34 +0000 From: Yubo Fan Organization: Chemistry Department, Texas A&M University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: zh-CN, en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: TVector option in G98 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, everyone, I am interested in TVector=N option in optimization process but it cannot work properly. Any suggestion? I will summerize. Thanks in advance. Yubo -- ============================================================ Yubo Fan Email: yubofan@mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-7222 Texas A&M University College Station, TX 77843 ============================================================ From chemistry-request@server.ccl.net Sun Mar 11 15:28:09 2001 Received: from usc.edu (root@usc.edu [128.125.253.136]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2BKS9w05417 for ; Sun, 11 Mar 2001 15:28:09 -0500 Received: from rcf-fs.usc.edu (root@rcf-fs.usc.edu [128.125.253.166]) by usc.edu (8.9.3.1/8.9.3/usc) with ESMTP id MAA26227; Sun, 11 Mar 2001 12:28:09 -0800 (PST) Received: from usc.edu (IDENT:jorgevil@futura.usc.edu [128.125.14.59]) by rcf-fs.usc.edu (8.9.3.1/8.9.3/usc) with ESMTP id MAA08359; Sun, 11 Mar 2001 12:28:08 -0800 (PST) Sender: jorgevil@rcf-fs.usc.edu Message-ID: <3AABDFD9.B219DBF4@usc.edu> Date: Sun, 11 Mar 2001 12:28:09 -0800 From: Jordi Villa X-Mailer: Mozilla 4.61 [en] (X11; I; Linux 2.2.12-20 i686) X-Accept-Language: en MIME-Version: 1.0 To: Mao Xiang CC: "chemistry@ccl.net" Subject: Re: CCL:how to derive reliable charge in AMSOL References: <3AAA2A12.C09C2FE4@iris.sipp.ac.cn> Content-Type: multipart/alternative; boundary="------------803F878C1D8739A8736B12B4" --------------803F878C1D8739A8736B12B4 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Mao Xiang, If the charges you are interested in are only those for the substrate or a relatively small number of atoms I would recommend you to follow the procedure for obtaining charges for a chemsol calculation. This is, use PCM with high level ab initio calculations in Gaussian and obtain the ESP charges. We have seen that these are the more reliable charges for our calculations. See Langevin Dipoles Model for ab Initio Calculations of Chemical Processes in Solution: Parameterization and Application to Hydration Free Energies of Neutral and Ionic Solutes and Conformational Analysis in Aqueous Solution, J. Florián and A. Warshel, J. Phys. Chem. 101, 5583-5595 (1997). Calculations of Hydration Entropies of Hydrophobic, Polar, and Ionic Solutes in the Framework of the Lnagevin Dipoles Solvation Model, J. Florián and A. Warshel, J. Phys. Chem. B, 103, 10282-10288 (1999) . Hope this helps Jordi Mao Xiang wrote: > Hello all: > I am using polaris from Dr. Warlsh to stduy the reaction in enzyme. > In this package, it need the atomic charge in the simulation. I think it > is better to derive them in AMSOL package, but there are many possible > ways to derive the charge in amsol using different keywords. So I wonder > if there are some suggestion about which keywords would give me some > reliable atomic charge. Thanks in advance. > > Regards, > mao xiang > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > | Xiang Mao | > | Lab of Molecular Regulation for Microbial Secondary Metabolism | > | Shanghai institute of Plant Physiology, Academia Sinica | > | 300 Fenglin Road, Shanghai, China, 200032 | > | Tel: +86-21-64042090-4791 | > | Fax: +86-21-64042385 | > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > -= 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 -- Jordi Villa i Freixa jorgevil@usc.edu http://laetro.usc.edu/wgroup/people/jorgevil Department of Chemistry, University of Southern California Los Angeles, CA, USA, 90089-1062 Tlf: 1-(213)-740 7671 Fax: 1-(213)-740 2701 --------------803F878C1D8739A8736B12B4 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Mao Xiang,

If the charges you are interested in are only those for the substrate or a relatively small number of atoms I would recommend you to follow the procedure for obtaining charges for a chemsol calculation. This is, use PCM with high level ab initio calculations in Gaussian and obtain the ESP charges. We have seen that these are the more reliable charges for our calculations.

See

Langevin Dipoles Model for ab Initio Calculations of Chemical Processes in Solution: Parameterization and Application to Hydration Free Energies of Neutral and
     Ionic Solutes and Conformational Analysis in Aqueous Solution, J. Florián and A. Warshel, J. Phys. Chem. 101, 5583-5595 (1997).

Calculations of Hydration Entropies of Hydrophobic, Polar, and Ionic Solutes in the Framework of the Lnagevin Dipoles Solvation Model, J. Florián and A. Warshel, J.
     Phys. Chem. B, 103, 10282-10288 (1999) .

Hope this helps

Jordi

Mao Xiang wrote:

Hello all:
    I am using polaris from Dr. Warlsh to stduy the reaction in enzyme.
In this package, it need the atomic charge in the simulation. I think it
is better to derive them in AMSOL package, but there are many possible
ways to derive the charge in amsol using different keywords. So I wonder
if there are some suggestion about which keywords would give me some
reliable atomic charge. Thanks in advance.

Regards,
mao xiang

  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|  Xiang Mao                                                     |
|  Lab of Molecular Regulation for Microbial Secondary Metabolism |
|  Shanghai institute of Plant Physiology, Academia Sinica        |
|  300 Fenglin Road, Shanghai, China, 200032                      |
|  Tel: +86-21-64042090-4791                                      |
|  Fax: +86-21-64042385                                           |
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

-= 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

-- 
Jordi Villa i Freixa                  
jorgevil@usc.edu   http://laetro.usc.edu/wgroup/people/jorgevil
Department of Chemistry, University of Southern California
Los Angeles, CA, USA, 90089-1062
Tlf: 1-(213)-740 7671 Fax: 1-(213)-740 2701
  --------------803F878C1D8739A8736B12B4-- From chemistry-request@server.ccl.net Mon Mar 12 07:44:01 2001 Received: from mailgw.cica.es (erika.cica.es [150.214.1.3]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2CCi0w08758 for ; Mon, 12 Mar 2001 07:44:00 -0500 Received: from simulux.us.es (IDENT:root@simulux.us.es [150.214.145.66]) by mailgw.cica.es (8.9.1/8.9.3) with ESMTP id NAA19731; Mon, 12 Mar 2001 13:43:58 +0100 (MET) Received: from localhost (rafapa@localhost) by simulux.us.es (8.9.3/8.9.3) with ESMTP id OAA15891; Mon, 12 Mar 2001 14:47:53 +0100 Date: Mon, 12 Mar 2001 14:47:53 +0100 (CET) From: Rafael Rodriguez Pappalardo To: Lars Packschies cc: chemistry@ccl.net Subject: Re: CCL:Redhat/G98/PGI - Error In-Reply-To: <20010312111419.E19987@campfire.rrz.Uni-Koeln.DE> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 12 Mar 2001, Lars Packschies wrote: > Dear CCLers, > > I'm trying to compile g98.A7 on a Redhat 7.0 (ok, not the best choice). > PGF77 ist working fine (as far I coud see). But when it comes to > build/link l402, I get an error. The text is attached. > > Is this a RH7-specific problem which means to install a different > distribution ? > It wouldn't surprise me anayway... Is anybody out there who compiled > g98.A7 on a RH7 PIII-box ? > > Thanks in advance, > > Lars > > Hi!, just delete bd0402.o in bsd/i386.make line: $(RUNF77) $(FFLAGS) -o $*.exe m$*.o $(EXTOBJ) $*.a bd0402.o $(EXTRAS) $(GAULIB) $(LIBS) Apparently the RH 7.0 linker does not need the block data outside of a library file. I presume the same problem arise in l609 and l809. Rafael -- Dr. Rafael R. Pappalardo Dept. Quimica Fisica, Fac. de Quimica, Univ. de Sevilla. 41012-Sevilla (Spain) e-mail: rafapa@simulux.us.es From chemistry-request@server.ccl.net Mon Mar 12 09:29:33 2001 Received: from mail2.zrz.tu-berlin.de (mail2.zrz.TU-Berlin.DE [130.149.4.14]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2CETXw09238 for ; Mon, 12 Mar 2001 09:29:33 -0500 Received: from mailszrz.zrz.tu-berlin.de ([130.149.4.11]) by mail2.zrz.tu-berlin.de with esmtp (exim-3.22) id 14cTKD-0001mM-00; Mon, 12 Mar 2001 15:29:29 +0100 Received: from natrium.chem.tu-berlin.de ([130.149.42.210]) by mailszrz.zrz.tu-berlin.de with esmtp (exim-3.22) id 14cTKD-0003g1-00; Mon, 12 Mar 2001 15:29:29 +0100 Mime-Version: 1.0 X-Sender: chwu0531@mailszrz.zrz.tu-berlin.de Message-Id: In-Reply-To: <20010312111419.E19987@campfire.rrz.Uni-Koeln.DE> References: <20010312111419.E19987@campfire.rrz.Uni-Koeln.DE> Date: Mon, 12 Mar 2001 15:29:37 +0100 To: Lars Packschies From: Christoph van =?iso-8859-1?Q?W=FCllen?= Subject: Re: CCL:Redhat/G98/PGI - Error Cc: chemistry@ccl.net Content-Type: text/plain; charset="us-ascii" ; format="flowed" >Dear CCLers, > >I'm trying to compile g98.A7 on a Redhat 7.0 (ok, not the best choice). >PGF77 ist working fine (as far I coud see). But when it comes to >build/link l402, I get an error. The text is attached. > >Is this a RH7-specific problem which means to install a different >distribution ? >It wouldn't surprise me anayway... Is anybody out there who compiled >g98.A7 on a RH7 PIII-box ? > This is a well-known problem (at least, I helped others in some occasions). The problem is the linking of a block-data unit. To enforce linking, g98.make first extracts bd0402.o from the archive l402.a, and then links the program with bd0402.o against l402.a. This causes the multiple definition errors. (Note to gaussian: very silly programming). You have to make a local copy of l402.a, then extract *and* delete bd0402.o, and if you are ready, do not forget to restore l402.a. Here my suggestion for g98.make (do not copy the comments with <=====). l402.exe: $(EXTRAS) l402.a $(RUNFSP) -e m$* $(BSDDIR)/main.F $(RUNMAKE) $(MAKELOC) OPTFLAG='$(OPTFLAG)' $(EXTRAS) $*.a m$*.o cp l402.a local402.a <=== MAKE LOCAL COPY ar x l402.a bs0402.o ar d l402.a bs0402.o <=== DELETE bd0402.a from l402.a $(RUNF77) $(FFLAGS) -o $*.exe m$*.o $(EXTOBJ) $*.a bd0402.o $(EXTRAS) $( GAULIB) $(LIBS) rm -f m$*.* bd0402.o mv local402.a l402.a <=== RESTORE l402.a Try it. If it works, tell me. -- +---------------------------------+-------------------------------------+ | Prof. Christoph van Wullen | Tele-Phone (+49) (0)30 314 27870 | | Technische Universitat Sekr. C3 | Tele-Fax (+49) (0)30 314 23727 | | Strasse des 17. Juni 135 | eMail | | D-10623 Berlin, Germany | Christoph.vanWullen@TU-Berlin.De | +---------------------------------+-------------------------------------+ From chemistry-request@server.ccl.net Mon Mar 12 10:45:50 2001 Received: from compchem.dfh.dk (compchem.dfh.dk [130.225.225.51]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2CFjnw09602 for ; Mon, 12 Mar 2001 10:45:50 -0500 Received: (from jeremy@localhost) by compchem.dfh.dk (SGI-8.9.3/8.9.3) id QAA39400 for chemistry@ccl.net; Mon, 12 Mar 2001 16:43:51 +0100 (MET) Date: Mon, 12 Mar 2001 16:43:51 +0100 From: Jeremy Greenwood To: chemistry@ccl.net Subject: GAMESOL, IRIX6.5, mips4, MPI Message-ID: <20010312164350.A239271@compchem.dfh.dk> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 1.0i Dear CCL, and specifically Gamesol users, I'd like to hear from people who have successfully compiled a mips4/64 bit Gamesol-v3.0 version for Irix6.5 I have built a working executable, (Irix6.5.10, Octane, 2 195 MHZ IP30 Processors CPU: MIPS R10000 Processor Chip Revision: 2.7) based on the recommended 'July 11, 2000' version of GAMESS, and using the DDI/System V shared memory, MPI and array installations, plus GAMESS patches supplied by SGI for the closest date: http://www.sgi.com/chembio/resources/gamess_us/25oct2000.html (I failed to build a working 64 bit executable without these patches.) The GAMESS tests all pass, but three of the Gamesol test series bomb, Input.sysv/test1.08.out: *** ERROR TERMINATION *** Input.sysv/test1.18.out: *** ERROR TERMINATION *** Input.sysv/test13a.out: *** ERROR TERMINATION *** all during the same routine: EIGENVECTOR ROUTINE EINVIT DID NOT CONVERGE FOR VECTOR 34. NORM = 4.73E-16 PERFORMANCE INDEX = 1.07E+13 (AN ERROR HALT WILL OCCUR IF THE PI IS GREATER THAN 100) EINVIT HAS FAILED TO CONVERGE FOR VECTOR 34 UNABLE TO DIAGONALIZE IN COPROJ EXECUTION OF GAMESS TERMINATED ABNORMALLY AT Fri Mar 9 05:14:05 2001 A mips2/32 bit version on the same machine doesn't suffer these errors, and gives results that are almost identical to the supplied test outputs, which were run on an Origin2 (though these output files say 'IRIX64') Hope someone has been down this path before and can suggest a fix... Jeremy ---------------------------------------------------------------------- Jeremy Greenwood jeremy.greenwood@i.am Department of Medicinal Chemistry bh +45 35306117 Royal Danish School of Pharmacy fx +45 35306040 Universitetsparken 2, DK-2100 Copenhagen, Denmark ah +45 32598030 ---------------------------------------------------------------------- From chemistry-request@server.ccl.net Mon Mar 12 17:28:45 2001 Received: from gpo.cam.msi-eu.com (cam.msi-eu.com [192.190.183.254]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f2CMSiw11663 for ; Mon, 12 Mar 2001 17:28:45 -0500 Received: from bonanza (dial131.cam.msi-eu.com [172.27.131.131]) by gpo.cam.msi-eu.com (8.9.3/8.9.3/Debian 8.9.3-21) with ESMTP id WAA21348 for ; Mon, 12 Mar 2001 22:26:41 GMT X-Authentication-Warning: gpo.cam.msi-eu.com: Host dial131.cam.msi-eu.com [172.27.131.131] claimed to be bonanza Message-Id: <4.2.2.20010312221552.00ccdde0@mailhost.cam.msi-eu.com> X-Sender: phil_hastings@mailhost.cam.msi-eu.com X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.2 Date: Mon, 12 Mar 2001 22:25:43 +0000 To: chemistry@ccl.net From: Phil Hastings Subject: MSI Materials Studio workshop at Spring ACS Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Materials Studio Introduction and Training Event Molecular Simulations Inc. will hold two half day Materials Studio training events alongside the annual American Chemical Society meeting in San Diego in April. These will be conveniently located in a hotel near the ACS venue, and there will be no charge for attending. You are cordially invited to attend either the morning or afternoon session on Tuesday April 3rd to learn about the exciting possibilities offered by Materials Studio. Please note that, since space is limited, you must register on the on-line registration form (URL given below). Materials Studio is dedicated to the modeling of a wide range of materials systems including small molecules, organic and inorganic crystals, polymers and semi-conductors. It is a modular package consisting of Materials Visualizer, the core module offering sophisticated building and visualization capabilities, with separate plugin application modules such as Discover, for classical mechanics simulations, and Reflex, for powder diffraction work. On hand will be MSI staff to help answer your questions, so please come along and try out the Materials Studio range! To register for the hands-on training, please go to http://www.msi.com/about/events/acs/register.html For more information about Materials Studio, please visit the webpages at http://www.materials-studio.com We look forward to seeing you in San Diego. Sincerely, Phil Hastings ****************************************** Dr Phil Hastings Product Manager, Materials Studio Molecular Simulations Ltd 230/250 The Quorum Barnwell Road Cambridge CB5 8RE England Tel: +44 1223 402851 Fax: +44 1223 413301 Website: http://www.msi.com ****************************************** From chemistry-request@server.ccl.net Mon Mar 12 18:37:10 2001 Received: from tbone.agouron.com (tbone.agouron.com [198.182.177.3]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f2CNb9w11916 for ; Mon, 12 Mar 2001 18:37:09 -0500 Received: from relay.agouron.com by tbone.agouron.com via smtpd (for server.ccl.net [192.153.40.39]) with SMTP; 12 Mar 2001 23:37:10 UT Received: from quarter.agouron.com (quarter.agouron.com [10.0.7.54]) by dns3.agouron.com (8.9.3/8.9.3) with ESMTP id PAA41129; Mon, 12 Mar 2001 15:39:30 -0800 (PST) Received: by quarter.agouron.com with Internet Mail Service (5.5.2650.21) id ; Mon, 12 Mar 2001 15:36:17 -0800 Message-ID: <074CA135830AD411BA7A00D0B741D25A021FAE55@CAMBIO> From: "Burke, Ben" To: "'Danilo Gonzalez'" , CHEMISTRY@ccl.net Subject: RE: Ligand binding to protein (DeltaH=0) Date: Mon, 12 Mar 2001 15:36:38 -0800 Dear Danilo: The post from David Turner titled "Protease Inhibitors Entropy/Enthalpy" has a number of examples where the reaction is entropically driven (but the enthalpy was not necessarily equal to 0.00). It was posted a couple of weeks ago (2/27). The Freire articles outline some nice thermodynamic characterization of these systems. Best to you, --Ben ---------------------------------------------------------------------- Benjamin J. Burke Pfizer Global R&D La Jolla burke@agouron.com Senior Scientist 10777 Science Center Dr Tel (858)622-3018 Computational Chemistry San Diego,CA 92121-1111 FAX (858)678-8244 -----Original Message----- From: Danilo Gonzalez [mailto:fgonzale@lauca.usach.cl] Sent: Friday, March 02, 2001 8:52 AM To: CHEMISTRY@ccl.net Subject: CCL:Ligand binding to protein (DeltaH=0) I'm looking for references about systems where ligand binding to protein is carried out with Delta H = 0, that is, where the process is Entropically driven.