From chemistry-request@server.ccl.net Fri Oct 8 04:01:49 1999 Received: from Mercury.acs.unt.edu (mercury.acs.unt.edu [129.120.220.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA05148 for ; Fri, 8 Oct 1999 04:01:48 -0400 Received: from jove.acs.unt.edu (6930@jove.acs.unt.edu [129.120.220.41]) by Mercury.acs.unt.edu (8.8.8/8.8.8) with ESMTP id CAA03130 for ; Fri, 8 Oct 1999 02:57:47 -0500 (CDT) Received: from localhost (aiz0001@localhost) by jove.acs.unt.edu (8.8.8/8.8.8) with ESMTP id CAA06294 for ; Fri, 8 Oct 1999 02:57:46 -0500 (CDT) Date: Fri, 8 Oct 1999 02:57:45 -0500 (CDT) From: Anita Ilze Zvaigzne To: chemistry@ccl.net Subject: CCL: Question About Structure/Viewing Software Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL-ers: I have limited funds, and thus, I am on a shoestring budget. I want to generate 2D chemical structures that can be pasted into Microsoft Word 97 and PowerPoint for publication in a refereed journal and for electronic dissemination on the Web. Also, I have a PDB-type file generated by using AMBER, and I want to prepare a 3D image that can be pasted into Microsoft Word 97 as well as PowerPoint for the purpose of publication. Could anyone point me to the best software that would achieve these goals? I realize that this is not really a computational chemistry question, but perhaps some of you have some suggestions anyway. Thanks. Respectfully, Anita I. Zvaigzne From chemistry-request@server.ccl.net Fri Oct 8 07:46:51 1999 Received: from iris.sipp.ac.cn ([202.127.25.14]) by server.ccl.net (8.8.7/8.8.7) with SMTP id HAA06984 for ; Fri, 8 Oct 1999 07:46:34 -0400 Received: from iris.sipp.ac.cn (202.127.25.133) by iris.sipp.ac.cn (EMWAC SMTPRS 0.81) with SMTP id ; Fri, 08 Oct 1999 19:45:14 +0800 Sender: user@ccl.net Message-ID: <37FDC953.D44562F2@iris.sipp.ac.cn> Date: Fri, 08 Oct 1999 19:37:07 +0900 From: mao xiang Organization: iris.sipp.ac.cn X-Mailer: Mozilla 4.05C-SGI [en] (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: chemistry@ccl.net Subject: problem of zwitterion TS search Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, everyone: I have met a problem in TS search. And the deduced TS is a zwitterion. And are there someone that have the experiences about solving this kind of problem. I have read the manual of mopac, it mentions the COSMO. I set the NSPA=60,GRADIENTS,1SCF,EPS=78.4,AM1 in the input file, and it seems that the mopac( from insight97.0) does not accept the keywords of NSPA,EPS.So I do not know how to use it in MOPAC. Hope you can give me some suggestion. Thanks in advance. Sincerely, Mao Xiang ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | Mao Xiang | | 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 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Fri Oct 8 08:50:30 1999 Received: from thanatos.sovam.com (thanatos.sovam.com [194.67.1.159]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA07276 for ; Fri, 8 Oct 1999 08:50:28 -0400 Received: from nnfalcon.glas.apc.org ([193.124.5.42]:47350 "EHLO nnfalcon.glas.apc.org" ident: "NO-IDENT-SERVICE[2]" whoson: "-unregistered-" smtp-auth: TLS-CIPHER: TLS-CCERT: ) by thanatos.sovam.com with ESMTP id ; Fri, 8 Oct 1999 16:45:55 +0400 Received: from localhost(chembr.mitht.rssi.ru[193.232.216.226]) (1115 bytes) by nnfalcon.glas.apc.org via sendmail with P:smtp/R:smart_host/T:smtp (sender: ) id for ; Fri, 8 Oct 1999 16:45:49 +0400 (MSD) (Smail-3.2.0.108 1999-Sep-19 #2 built 1999-Sep-20) Received: from komkon3 ([192.168.1.23]) by chembridge.ru with SMTP id 1478 for ; Fri, 8 Oct 1999 16:45:41 +0400 X-Mail-Server: Eserv/2.5 /Unregistered Message-ID: <001901bf1193$69279650$1701a8c0@komkon3> From: "Gennady Makeev" To: References: <37FDC953.D44562F2@iris.sipp.ac.cn> Subject: Algorithms of substructural search. Date: Fri, 8 Oct 1999 16:45:40 +0300 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Hi, everyone! I'm interested in description of substructure search algorithms or realisation of the algorithms as free subroutines wirtten in C/C++/Java and so on. All answers will be appreciated and useful ones will be summarized. Gennady Makeev From chemistry-request@server.ccl.net Fri Oct 8 09:33:53 1999 Received: from ns2.nycap.rr.com (root@prefetch-atm.nycap.rr.com [24.92.32.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA07460 for ; Fri, 8 Oct 1999 09:33:53 -0400 Received: from claessen.nycap.rr.com (cm-24-29-72-56.nycap.rr.com [24.29.72.56]) by ns2.nycap.rr.com (8.9.3/8.9.3) with SMTP id JAA24913; Fri, 8 Oct 1999 09:29:37 -0400 (EDT) Reply-To: From: "Rolf Claessen" To: "Anita Ilze Zvaigzne" , Subject: RE: Question About Structure/Viewing Software Date: Fri, 8 Oct 1999 09:29:54 -0400 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit 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 V4.72.3612.1700 In-Reply-To: Dear Dr. Zvaigzne, a very good free 2D structure program is ISIS Draw and for visualization I would recommend the free program swissPDB in combination with POV Ray (also free and maybe the best raytracer). This combination produces gorgeous pictures. Find these programs and many more free and commercial prgrams listed at http://www.claessen.net/chemistry/soft_en.html Regards, Rolf Claessen > -----Original Message----- > From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On > Behalf Of Anita Ilze Zvaigzne > Sent: Friday, October 08, 1999 3:58 AM > To: chemistry@ccl.net > Subject: CCL:Question About Structure/Viewing Software > > > Dear CCL-ers: > > I have limited funds, and thus, I am on a shoestring budget. I want > to generate 2D chemical structures that can be pasted into Microsoft Word > 97 and PowerPoint for publication in a refereed journal and for > electronic dissemination on the Web. Also, I have a PDB-type file > generated by using AMBER, and I want to prepare a 3D image that can be > pasted into Microsoft Word 97 as well as PowerPoint for the purpose of > publication. > > Could anyone point me to the best software that would achieve these > goals? I realize that this is not really a computational chemistry > question, but perhaps some of you have some suggestions anyway. Thanks. > > Respectfully, > Anita I. Zvaigzne > > > -= 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 Fri Oct 8 09:48:28 1999 Received: from theory.tc.cornell.edu (THEORY.TC.CORNELL.EDU [128.84.30.174]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA07558 for ; Fri, 8 Oct 1999 09:48:28 -0400 Received: from ren.tc.cornell.edu (REN.TC.CORNELL.EDU [128.84.20.129]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with SMTP id JAA24655; Fri, 8 Oct 1999 09:44:30 -0400 Sender: richard@tc.cornell.edu Message-ID: <37FDF53E.3F54@tc.cornell.edu> Date: Fri, 08 Oct 1999 09:44:30 -0400 From: Richard Gillilan X-Mailer: Mozilla 3.01SC-SGI (X11; I; IRIX 6.2 IP22) MIME-Version: 1.0 To: Joe M Leonard CC: chemistry@ccl.net Subject: Re: CCL:PLP - piecewise linear potential? References: <199910071520.LAA10237@world.std.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Joe M Leonard wrote: > > Folks, > > I am trying to parse my notes from ACS, New Orleans, and I wonder > whether anybody has references to the PLP docking/scoring function > which was mentioned by several speakers. I think this is the > "piecewise linear potential" method, but I'm not sure of this... > The idea is simple. Just pre-evaluate the potential on a grid and use trilinear interpolation. Several docking programs out there use piecewise linear approximations to the potential (or forces) on a regular grid: Autodock (Goodsell and Olson) Proteins: Structure, Function and Genetics 8:195-202 (1990) FlexX (Luty, Wasserman, Stouten and Hodge) J. Comp. Chem. Vol 16, No 4 454-464 (1995) (I'm pretty sure there are several others, but I can't find the refs at the moment. The method has also been used in material science simulations) Also, Oberlin, Trosset and Scheraga have used cubic B-splines on a regular grid with great success (Prodock). This method allows for larger grid elements with better accuracy, C2 continuity (smooth derivatives) and overall greater smoothness which seems to improve the search efficiency: Oberlin, Scheraga J. Comp. Chem. Vol 19 No 1 pp 71-85 (1998) Trosset, Scheraga J. Comp. Chem. Vol 20 No 4 pp 412-427 (1999) I've implemented this technique in OrderFour, my own MMFF-based docking and simulation code. I'm also experimenting with adaptive and hierarchical grids for use in multi-body protein-protein docking. OrderFour will be generally available as open-source (I will read-enable the revision control system) as soon as I can get a paper out and get final approval from CTC. We are still making major revisions to the API so it's still too early to invite external users to help work on the code, but I'll make a general announcement when things are ready some time this winter. Richard Richard Gillilan (richard@tc.cornell.edu) Cornell Theory Center From chemistry-request@server.ccl.net Thu Oct 7 18:49:55 1999 Received: from web702.mail.yahoo.com (web702.mail.yahoo.com [128.11.23.22]) by server.ccl.net (8.8.7/8.8.7) with SMTP id SAA03252 for ; Thu, 7 Oct 1999 18:49:54 -0400 Message-ID: <19991007225221.7185.rocketmail@web702.mail.yahoo.com> Received: from [141.161.231.62] by web702.mail.yahoo.com; Thu, 07 Oct 1999 15:52:21 PDT Date: Thu, 7 Oct 1999 15:52:21 -0700 (PDT) From: Aaron First Subject: For APROPOS program To: CHEMISTRY@server.ccl.net Cc: aaronguyue@yahoo.com MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi,CCLers, I have read the paper by Peters KP, Fauck J, and Frommel C mentioned the program APROPOS (JMB,1996) which can search PDB files for ligand binding sites. It is said that this program is available for SGI machines on request from the authors. But I could not find the email adresses of the authors. Is there anybody who know the authors and kindly give me their email addresses? BEst regards, Aaron ===== __________________________________________________ Do You Yahoo!? Bid and sell for free at http://auctions.yahoo.com From chemistry-request@server.ccl.net Thu Oct 7 22:13:59 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA03888 for ; Thu, 7 Oct 1999 22:13:59 -0400 Received: from csb0.IPC.PKU.EDU.CN (csb0.ipc.pku.edu.cn [162.105.177.12]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with SMTP id WAA19351 for ; Thu, 7 Oct 1999 22:10:03 -0400 (EDT) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA06846; Fri, 8 Oct 99 10:09:34 -0700 Date: Fri, 8 Oct 1999 10:09:29 -0700 (PDT) From: Tao Peng To: ccl Subject: Summary:How to call a C++ program from C? Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII About two weeks ago, I have submited the following question: Dear All, I have a big program which is written in C and Fortran, but mainly in C. The author compile each module by their own compiler ( cc and f77 on SGI) and link them by f77. Now I have another C++ program (still others) and want incorporate it into the previous big program. My idea is want to call C++ from C, but compile them separately, and link them altogether. Can anyone tell me whether this idea is possible, or have better suggestion? Now I have received the following replies: 1) Ernest Friedman-Hill C can call C++ routines which are declared as extern "C", but no others. 2) From: hinsen@dirac.cnrs-orleans.fr This is difficult, and certainly not possible in a portable way. Mixing C and Fortran is easy, but you should use f77 to link (on some systems this is not strictly necessary; adding the Fortran libraries when linking is sufficient). Mixing C and C++ is also easy, but you must use CC to link. So for mixing C with C++ and Fortran, you'd have to link with both CC and f77. The reason for this problem is that both C++ and Fortran program often need specific initialization code that is added during linking. An added complication with C++ is name mangling (the compiler must create unique names for overloaded functions etc.), but there are ways around that. In summary, what you are trying to do is possible only on a system that allows calling Fortran from C without any special initialization code for Fortran. I don't know whether this is true for SGI systems. -- 3) From: Jochen On Mit, 29 Sep 1999 hinsen@dirac.cnrs-orleans.fr wrote: >> I have a big program which is written in C and Fortran, but mainly in C. >> The author compile each module by their own compiler ( cc and f77 on SGI) >> and link them by f77. >> >> Now I have another C++ program (still others) and want incorporate it >> into the previous big program. >The reason for this problem is that both C++ and Fortran program often >need specific initialization code that is added during linking. An >added complication with C++ is name mangling (the compiler must create >unique names for overloaded functions etc.), but there are ways around >that. Hi Konrad, you are right - as usual :-) Many times you can resolve the explained problems by incremental linkage (like ld -r), though. So you link all your FORTRAN code into one big object file using the FORTRAN compiler as linker driver, analogous the C++ code using the C++ linker driver. Then you link these into the final exectuable. The only remaining problem I ever encountered is some trouble about a duplicate or no main function. -- Jochen Thanks for all the help!!! Have a nice day! Yours Sincerely Tao Peng \*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\* \* \* \* Tao Peng \* \* \* \* Molecular Design Laboratory \* \* Institute of Physical Chemistry \* \* Peking University \* \* Beijing, 100871 \* \* P.R.China \* \* \* \* E-mail:taop@csb0.ipc.pku.edu.cn \* \* Lab Phone: 86-10-62756833 \* \* Fax Number:86-10-62751725 \* \* http://www.ipc.pku.edu.cn/~taop/ \* \* Address:Peking University Building 46 Room 2122 \* \* Dormitory Phone: 86-10-62761206 \* \*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\* From chemistry-request@server.ccl.net Thu Oct 7 23:18:59 1999 Received: from caxton.correionet.com.br (caxton.correionet.com.br [200.246.35.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA04136 for ; Thu, 7 Oct 1999 23:18:45 -0400 Received: from dasf (cnet63-099.correionet.com.br [200.246.63.99]) by caxton.correionet.com.br (8.9.3/8.9.3) with SMTP id XAA77668 for ; Thu, 7 Oct 1999 23:23:43 -0200 (EDT) Message-Id: <4.1.19991006231445.00966550@mailhost.correionet.com.br> X-Sender: dasf@mailhost.correionet.com.br X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Wed, 06 Oct 1999 23:16:30 -0300 To: CHEMISTRY@ccl.net From: =?iso-8859-1?Q?=22Dem=E9trio_A=2E_da_Silva_Filho=22?= (by way of =?iso-8859-1?Q?Dem=E9trio?= FIlho ) Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id XAA04137 Dear Colleagues, I'm trying to compile G94 under OSF1 V4.0 564 alpha and I'm getting the folowing error message: if ( 1 ) make -f bsd/g94.make JUNK1=JUNK make -f bsd/g94.make JUNK1=JUNK gau-cpp -DALPHA_OSF1 -DI64 -DUSE_SYSV -DDEFMAXSHL=2500 -DDEFMAXATM=1000 -DDEFMAXNZ=1200 -DDEFNVDIM=257 -DDEFARCREC=1024 -DDEFLMAX=13 -DDEFCACHE=128 -DDEFN3MIN=10 -DDEFMAXOP=120 -DMERGE_LOOPS -DGAUSS_PAR -DGAUSS_THPAR -DONE_BACKSH -DLITTLE_END bsd/gau-worker.f ./gau-worker.f f77 -O5 -i8 -r8 -align dcommons -tune host -threads -assume noaccuracy_sensitive -c gau-worker.f rm -f gau-worker.f f77 -O5 -i8 -r8 -align dcommons -tune host -threads -assume noaccuracy_sensitive -o gau-worker gau-worker.o util.a -ldxml ld: Can't locate file for: -ldxml fort: Severe: Failed while trying to link. *** Exit 1 Stop. if ( -e gauopt ) rm -f gauopt ln -s g94opt gauopt ln: gauopt exists, specify -f to remove. Does anybody knows what is causing this problem and how can I solve that? It looks like I don't have the dxml library. It's possible to get something free to overcome this problem? Thanks in advance, Dasf _____________________________________ Demetrio A. da Silva Filho UNICAMP - IFGW Prédio D - Sala 17 CEP 13083-970 C.Postal 6165 Campinas - SP - Brasil _____________________________________ "Se não houver frutos, valeu a beleza das flores. Se não houver flores, valeu a sombra das folhas. Se não houver folhas, valeu a intenção da semente." Henfil From chemistry-request@server.ccl.net Fri Oct 8 06:27:05 1999 Received: from idun.phc.chalmers.se (idun.phc.chalmers.se [129.16.97.44]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA05822 for ; Fri, 8 Oct 1999 06:27:04 -0400 Received: from fkrs2.phc.chalmers.se (fkrs2.phc.chalmers.se [129.16.97.48]) by idun.phc.chalmers.se (8.8.8/8.8.7) with ESMTP id LAA20692 for ; Fri, 8 Oct 1999 11:23:09 +0100 Received: (from svedung@localhost) by fkrs2.phc.chalmers.se (8.8.8/8.8.8) id MAA14848; Fri, 8 Oct 1999 12:23:07 +0200 Date: Fri, 8 Oct 1999 12:23:05 +0200 (MDT) From: Harald Svedung To: CHEMISTRY@ccl.net Subject: summary Massage Scan Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi again! On tuesday i posted the following question and got the answers below: >> I'm trying to make as accurate calculations as possible on the interaction potentials between "atoms in molecules". I wish to make some BSSE-correction on some potential scans. I've tried the following for the colinear F2-F2 interaction: #RMP2/AUG-cc-pVTZ Scan Massage Test F-F F-F scan r2 0 1 F1 X1 F1 1. F2 F1 r1 X1 90. F3 F1 r2 X1 90. F2 180. X2 F3 1. F1 90. X1 180. F4 F3 r1 X2 90. F1 180. Variables: r2 1.10350222 6 0.1379377775 r1 1.40120372 3 Nuc 0.0 4 Nuc 0.0 as I want to use the basisfunctions on the second F2-molecule without the atoms to get a "maximum" correction for BSSE. Initially Gaussian seams to read this as taking away the second F2-molecule (output confirms 18 electrons), but when it comes to the scan it is confused regarding the numbering of the atoms and takes away not the second F2-molecule, but the F3 and X2 in the Z-matrix above. This results according to output in an odd number of electrons and thus a conflict with multiplicity. Is there a quick way arround this problem, some trivial keyword thing that I've missed or is this atom numbering missmatch in Gaussian a really unfortunate "feature"? << >From Joseph Ochterski at the helpdesk on Gaussian: >> It could be an unfortunate feature of the scan keyword. I think in this case, it's worth the effort of getting familiar with the MODREDUNDANT keyword. It really makes this case trivial. Here is a reformulation of your input deck. I've converted to cartesian coordinates, so the redundant internal coordinate code can build a Z-matrix that doesn't use dummy atoms. Then the atom numbering problem goes away. :) #P RMP2/aug-cc-pVTZ opt=modredundant massage Test F-F F-F scan r2 0 1 F 0.0000 0.0000 0.0000 F 0.0000 0.0000 1.40120372 F 0.0000 0.0000 2.50470594 F 0.0000 0.0000 3.90590966 1 2 F 3 4 F 2 3 S 6 0.1379377 3 Nuc 0.0 4 Nuc 0.0 -- Joseph Ochterski, Ph.D Senior Customer Service Scientist help@gaussian.com << Before that I got a quick and elegant solution to my special case from my office room-mate Stefan Andersson: >> #RMP2/AUG-cc-pVTZ Scan Massage Test F-F F-F scan r2 0 1 X1 X2 X1 r2 F1 X2 1. X1 90. F2 F1 r1 X2 90. X1 180. F3 X1 1. X2 90. F1 0. F4 F3 r1 X1 90. X2 180. Variables: r2 1.10350222 6 0.1379377775 r1 1.40120372 3 Nuc 0.0 4 Nuc 0.0 << In the first case dummy atoms are not used at all, and in the second the dummy atoms are simply put at t he top of the Z-matrix, thereby avoiding the "atom numbering problem" with the Scan keyword. Many thanks both of you! :-) /Harald Harald Svedung (Ph.Lic.) phone: +46-31-7722816 Department of Chemistry fax: +46-31-167194 Physical Chemistry home phone: +46-31-240897, +46-709223206 Goeteborg University home e-mail: harald.svedung@svedung.pp.se SE-412 96 Goeteborg, Sweden www.che.chalmers.se/~svedung/ From chemistry-request@server.ccl.net Fri Oct 8 13:14:39 1999 Received: from sumter.awod.com (sumter.awod.com [198.81.225.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA08742 for ; Fri, 8 Oct 1999 13:14:34 -0400 Received: from [208.140.97.72] (wa0072.tnt2.awod.com [208.140.97.72]) by sumter.awod.com (8.8.7/8.8.8) with SMTP id NAA02123; Fri, 8 Oct 1999 13:10:30 -0400 (EDT) (envelope-from netsci@awod.com) X-Sender: arichon@awod.com Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 8 Oct 1999 13:10:17 +0100 To: chemistry@ccl.net From: netsci@awod.com (Network Science) Subject: Student Stipend Awards Network Science Corporation, the host of The Charleston Conferences announces the second annual Network Science Student Stipend Award, co-sponsored by Cambridge Crystallographic Data Centre and Chemical Computing Group Advanced graduate students and post doctoral fellows are invited to submit an abstract for a poster presentation at one of the 2000 Conferences. The meetings are, Innovative Techniques for New Lead Discovery and Development (February 28-March 1), and Research Perspectives in Computational and Structural Chemistry (March 1-3). One award will be made for each of the two meetings. The student awards will include waiver of the conference registration fee along with a stipend to defray travel and accommodation expenses. Details are available as part of the conference announcement at http://www.netsci.org or by e-mailing editors@netsci.org From chemistry-request@server.ccl.net Fri Oct 8 17:28:59 1999 Received: from Jerry (sdn-ar-001nvlvegP243.dialsprint.net [206.133.195.5]) by server.ccl.net (8.8.7/8.8.7) with SMTP id RAA10305 for ; Fri, 8 Oct 1999 17:28:54 -0400 Date: Fri, 8 Oct 1999 17:28:54 -0400 From: Jerry Knaub To: Message-Id: <419.436441.59604259knaub@xts.net> Subject: Hello, Please enter Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Please enter our $100 WEEKLY drawing. Http://www.shopperindex.com We do not save, sell, or buy email address. Thank you very much Respond: Knaub@xts.net From chemistry-request@server.ccl.net Fri Oct 8 18:13:54 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA10551 for ; Fri, 8 Oct 1999 18:13:54 -0400 Received: from havana.ks.uiuc.edu (havana.ks.uiuc.edu [130.126.120.73]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id SAA24623 for ; Fri, 8 Oct 1999 18:09:49 -0400 (EDT) Received: from verdun.ks.uiuc.edu (verdun.ks.uiuc.edu [130.126.120.129]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with ESMTP id RAA13980 for ; Fri, 8 Oct 1999 17:09:50 -0500 (CDT) Received: from localhost (jim@localhost) by verdun.ks.uiuc.edu (8.9.1b+Sun/8.9.1) with ESMTP id RAA27362 for ; Fri, 8 Oct 1999 17:09:50 -0500 (CDT) X-Authentication-Warning: verdun.ks.uiuc.edu: jim owned process doing -bs Date: Fri, 8 Oct 1999 17:09:50 -0500 (CDT) From: Jim Phillips To: chemistry@www.ccl.net Subject: ANNOUNCE: NAMD 2.1b2 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII +--------------------------------------------------------------------+ | | | NAMD 2.1b2 Release Announcement | | | +--------------------------------------------------------------------+ October 8, 1999 The Theoretical Biophysics Group at the University of Illinois is proud to announce the public release of a new version of NAMD, a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code. NAMD development is supported by the NIH National Center for Research Resources. NAMD 2.1b2 is more stable than NAMD 2.0 and adds several new features: - Mollified impulse multiple timestepping method. - Faster particle mesh Ewald implementation. - Periodic boundaries for non-orthogonal cells. - New interactive molecular dynamics interface to VMD. NAMD is available from http://www.ks.uiuc.edu/Research/namd/. The Theoretical Biophysics group encourages NAMD users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. Any questions or comments may be directed to namd@ks.uiuc.edu. We are eager to hear from you, and thank you for using our software!