From chemistry-request@server.ccl.net Thu Aug 29 01:51:52 2002 Received: from cascara.uvic.ca (root@[142.104.5.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7T5pqr11022 for ; Thu, 29 Aug 2002 01:51:52 -0400 Received: from p17-99.dialup.uvic.ca (p17-99.dialup.uvic.ca [142.104.17.99]) by cascara.uvic.ca (8.12.4/8.12.4) with SMTP id g7T5piJE296232 for ; Wed, 28 Aug 2002 22:51:46 -0700 From: Roy Jensen To: chemistry@ccl.net Subject: SUMMARY: identifying single configuration systems Date: Wed, 28 Aug 2002 22:51:57 -0700 Message-ID: X-Mailer: Forte Agent 1.91/32.564 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-UVic-Virus-Scanned: OK - Passed virus scan by Sophos v3.59 X-Scanned-By: MIMEDefang 2.19 (www . roaringpenguin . com / mimedefang) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g7T5pqr11023 Thanks to those who responded. ORIGINAL QUESTION ************************************** Is it possible to tell, a priori, if a system can be reasonably and reliably represented by a single configuration method? Are there any systems that generally fail? transition states, partially filled orbitals, partially filled _degenerate_ orbitals, etc. RESPONSES ************************************** From: Karl Irikura Hi. I think you are OK as long as there are no low-lying excited states of the same (computational) irreducible representation. ************************************** From: Christoph van =?iso-8859-1?Q?W=FCllen?= a priori is difficult, but you may run an MP2 or CISD calculation and look at the occupation number of the natural orbitals. If they deviate substantially from 2.0 and 0.0 (say, less than 1.9, more than 0.1) this may be some indication for MR character. ************************************** From: elewars 2002 Aug 23 Hello, For a discussion of this see C. J. Cramer, "Essentials of Computational Chemistry", Wiley, 2002, chapters 6 and 7. From chemistry-request@server.ccl.net Wed Aug 28 14:59:47 2002 Received: from mail.interware.hu ([195.70.32.130]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7SIxlr10903 for ; Wed, 28 Aug 2002 14:59:47 -0400 Received: from caracas-0304.adsl.interware.hu ([195.70.61.48] helo=cthulhu) by mail.interware.hu with smtp (Exim 3.33 #1 (Debian)) id 17k82c-0000hn-00 for ; Wed, 28 Aug 2002 20:59:46 +0200 Message-ID: <005301c24ec5$48724f50$0200a8c0@cthulhu> From: "Tamas Gunda" To: Subject: chemory Date: Wed, 28 Aug 2002 21:01:14 +0200 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 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Dear CCL'ers, Not really CCL theme, rather education + fun in chemistry. I made a chemical memory card game called Chemory. The idea behind that I have quite sad experiences about the students' knowledge of practical (organic) chemistry - they know HOMO and LUMO, but fail when asking about xylene or ketoglutaric acid. So I tried to weld a teaching aid and some fun in the form of a memory game. Don't grin, the chemistry in it is not so easy! It is worth trying. It has two versions: free/trial and registrated shareware. In the latter it is possible to create new card template pages with ISIS/Draw. Have a look to http://web.interware.hu/frenzy/chemory Any feedback is welcomed, have fun, Dr. Tamas E. Gunda University of Debrecen Research Group for Antibiotics H-4010 Debrecen, POB 36 Hungary tamasgunda@tigris.klte.hu www.klte.hu/~gundat From chemistry-request@server.ccl.net Wed Aug 28 15:10:13 2002 Received: from gate-sl1.mdli.com ([208.200.221.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7SJACr11189 for ; Wed, 28 Aug 2002 15:10:12 -0400 Received: (from smap@localhost) by gate-sl1.mdli.com (8.8.8/8.8.8) id MAA00765; Wed, 28 Aug 2002 12:10:09 -0700 (PDT) Received: from puffin.mdli.com(172.16.1.12) by gate-sl1 via smap (V2.1) id xma000762; Wed, 28 Aug 02 12:10:06 -0700 Received: from exch-sl02.mdli.com by puffin.mdli.com (980427.SGI.8.8.8/BCH1.0) id MAA55239; Wed, 28 Aug 2002 12:10:06 -0700 (PDT) Received: by exch-sl02.mdli.com with Internet Mail Service (5.5.2653.19) id ; Wed, 28 Aug 2002 12:10:05 -0700 Message-ID: From: Keith Taylor To: Chemistry@ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, Eric_martin@chiron.com Subject: RE: XML and combinatorial chemistry Date: Wed, 28 Aug 2002 12:10:01 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) 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 g7SJADr11190 MDL is developing an XML replacement for the SDfile and RDfile. It will accommodate all of MDL's structure representations, including generic (Markush) structures, but it is not restricted to MDL structure formats. If you require more information please contact me directly at k.taylor@mdl.com. -----Original Message----- From: Stew Rubenstein [mailto:SRubenstein@cambridgesoft.com] Sent: Wednesday, August 28, 2002 7:18 AM To: Chemistry@ccl.net; CHMINF-L@LISTSERV.INDIANA.EDU; Eric_martin@chiron.com Subject: CCL:XML and combinatorial chemistry ChemDraw, ChemOffice, and other CambridgeSoft tools support XML representations and combinatorial chemistry. This also includes our library enumerator, plate inventory, BioAssay HTS, E-Notebook, and other applications. Please contact info@cambridgesoft.com to talk about this in more detail. -Stew Rubenstein President and CTO CambridgeSoft Corp. > -----Original Message----- > From: Shobe, Dave [mailto:dshobe@SUD-CHEMIEINC.COM] > Sent: Wednesday, August 28, 2002 9:36 AM > To: CHMINF-L@LISTSERV.INDIANA.EDU > Subject: FW: XML and combinatorial chemistry > > > Maybe someone in this community can answer this. Please reply to Eric > Martin directly as he might not read CHMINF-L regularly. > > --David Shobe > Süd-Chemie Inc. > phone (502) 634-7409 > fax (502) 634-7724 > email dshobe@sud-chemieinc.com > > Don't bother flaming me: I'm behind a firewall. > > > > -----Original Message----- > From: Martin, Eric [mailto:Eric_Martin@chiron.com] > Sent: Tuesday, August 27, 2002 7:51 PM > To: chemistry@ccl.net > Subject: CCL:XML and combinatorial chemistry > > > Dear CCL, > > Does CML or any other chemical XML application support combinatorial > chemistry? Specifically, I have in mind Markush or generic structures > with lists of R groups. Is specific support for Markush structures > necessary or > useful, or is there a way to do it with existing CML > elements? The CML FAQ > (http://www.xml-cml.org/faq/index.html) notes that "Heteromers" e.g. > modified proteins, are difficult to represent, which suggests > a Markush may > be as well. Thanks in advance. > > Regards, Eric > ___________________ > > Eric Martin > Chiron Corp, LSC 4.250 > 4560 Horton St. > Emeryville, CA 94608 > (510)923-3306 > FAX 923-2010 > > > > CHMINF-L Archives (also to join or leave CHMINF-L, etc.) > http://listserv.indiana.edu/archives/chminf-l.html > Search the CHMINF-L archives at: > http://listserv.indiana.edu/cgi-bin/wa?S1=chminf-l > Sponsors of CHMINF-L: > http://www.indiana.edu/~cheminfo/chminf-l_support.html > -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Thu Aug 29 04:57:43 2002 Received: from mailer.gwdg.de ([134.76.10.26]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7T8vgr19039 for ; Thu, 29 Aug 2002 04:57:43 -0400 Received: from vrlab03.mpibpc.gwdg.de ([134.76.211.99] helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtp (Exim 3.33 #12) id 17kL7R-0004XX-00 for chemistry@ccl.net; Thu, 29 Aug 2002 10:57:37 +0200 Message-ID: <3D6DE1D3.1090206@mpi-bpc.mpg.de> Date: Thu, 29 Aug 2002 10:56:51 +0200 From: Vlad Cojocaru User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4) Gecko/20011126 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: CCL list Subject: an explanation for freq. in Gaussian 94 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear CCLers, I must say that is the first time I am doing vibrational analysis. So I have a question. Below is an output from a Gaussian job. As far as I know for the structure to be a minimum all the freq must be positive...while a single negative value means a transition state. Please correct me if the case. I also read on Gaussian documentation that they are looking at how close to 0 are the low freq Now, the thing is that I can not really identify everything in this file. On one hand there is a row of low freq. close to 0 and other with positive but much larger values. As calculation proceeds there are other freq. calculated. Could somebody guide me a bit on interpreting this output??? Thanks a lot in advance!! Vlad Low frequencies --- -1.2692 -.4883 -.0004 .0008 .0009 1.9870 Low frequencies --- 35.8128 138.7204 164.2523 Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering activities (A**4/AMU), Raman depolarization ratios, reduced masses (AMU), force constants (mDyne/A) and normal coordinates: 1 2 3 ?A ?A ?A Frequencies -- 35.8117 138.7204 164.2523 Red. masses -- 1.0475 3.3764 5.3678 Frc consts -- .0008 .0383 .0853 IR Inten -- .0139 2.1122 5.4316 Raman Activ -- .1246 1.7291 .0713 Depolar -- .7372 .7499 .7106 Atom AN X Y Z X Y Z X Y Z 1 6 .00 .00 -.04 .00 .00 .26 .00 .00 .07 2 7 .00 .00 .03 .00 .00 -.12 .00 .00 -.13 3 6 .00 .00 .00 .00 .00 -.10 .00 .00 .19 4 1 .00 .00 .01 .00 .00 -.11 .00 .00 .39 5 7 .00 .00 -.01 .00 .00 -.08 .00 .00 .21 6 6 .00 .00 -.01 .00 .00 -.06 .00 .00 -.07 7 6 .00 .00 -.02 .00 .00 .17 .00 .00 -.08 8 7 .00 .00 -.01 .00 .00 .20 .00 .00 -.07 9 6 .00 .00 .01 .00 .00 .00 .00 .00 -.05 10 7 .00 .00 .02 .00 .00 -.11 .00 .00 -.28 11 6 .00 .00 .01 .00 .00 -.11 .00 .00 -.23 12 7 .00 .00 .02 .00 .01 -.10 -.01 -.01 .32 13 1 .00 .00 .01 .00 -.03 -.01 .06 .02 .51 14 1 .00 .00 .03 .00 -.03 -.25 .06 .02 .39 15 1 .00 .00 -.03 .00 .00 .33 .00 .00 -.05 16 1 .44 .19 -.36 .23 -.16 .26 .09 -.08 .09 17 1 -.47 -.21 -.29 -.25 .17 .28 -.10 .09 .09 18 1 .03 .02 .54 .02 -.01 .54 .01 -.01 .17 4 5 6 ?A ?A ?A Frequencies -- 233.0433 280.7473 386.2434 .............. -- Vlad Cojocaru Max Planck Institut for Biophysical Chemistry Deparment: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1389 e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de From chemistry-request@server.ccl.net Thu Aug 29 06:32:05 2002 Received: from salicet.ucd.ie ([137.43.1.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7TAW4r22715 for ; Thu, 29 Aug 2002 06:32:05 -0400 X-Confirm-reading-to: Laurence.Cuffe@ucd.ie X-PMrqc: 1 Received: from CONVERSION-DAEMON.Salicet.ucd.ie by Salicet.ucd.ie (PMDF V6.1-1 #40617) id <0H1L08A01P67YD@Salicet.ucd.ie> for chemistry@ccl.net; Thu, 29 Aug 2002 11:30:09 +0100 (IST) Received: from elvira.ucd.ie ([137.43.24.26]) by Salicet.ucd.ie (PMDF V6.1-1 #40617) with ESMTP id <0H1L07WIYP6766@Salicet.ucd.ie>; Thu, 29 Aug 2002 11:30:07 +0100 (IST) Date: Thu, 29 Aug 2002 11:30:30 +0100 From: Laurence Cuffe Subject: Re: CCL:an explanation for freq. in Gaussian 94 In-reply-to: <3D6DE1D3.1090206@mpi-bpc.mpg.de> To: Vlad Cojocaru , chemistry@ccl.net Message-id: <3D6E05D6.10346.FB02B3F@localhost> Organization: University College Dublin X-Mailer: Pegasus Mail for Win32 (v3.12c) Content-type: TEXT/PLAIN Priority: normal Date sent: Thu, 29 Aug 2002 10:56:51 +0200 From: Vlad Cojocaru Subject: CCL:an explanation for freq. in Gaussian 94 To: CCL list >Dear CCLers, > I must say that is the first time I am doing vibrational analysis. So >I have a question. Below is an output from a Gaussian job. As far as I >know for the structure to be a minimum all the freq must be >positive...while a single negative value means a transition state. >Please correct me if the case. > I also read on Gaussian documentation that they are looking at how >close to 0 are the low freq > Now, the thing is that I can not really identify everything in this >file. On one hand there is a row of low freq. close to 0 and other with >positive but much larger values. As calculation proceeds there are other >freq. calculated. > Could somebody guide me a bit on interpreting this output??? >Thanks a lot in advance!! >Vlad This output looks fine! The really low frequencies -1.26 -.4883 etc correspond to rotation and displacement modes and should be close to zero say < 3.0 these are and thus are nothing to worry about. All your proper frequencies (which are given with intensity information etc), are positive as they should be. A good source for more information is on the gaussian web site in the paper by Joseph W. Ochterski at http://www.gaussian.com/vib.htm Hope this helps Laurence Cuffe > > Low frequencies --- -1.2692 -.4883 -.0004 .0008 >>.0009 1.9870 > Low frequencies --- 35.8128 138.7204 164.2523 > Harmonic frequencies (cm**-1), IR intensities (KM/Mole), > Raman scattering activities (A**4/AMU), Raman depolarization ratios, > reduced masses (AMU), force constants (mDyne/A) and normal coordinates: > 1 2 3 > ?A ?A ?A > Frequencies -- 35.8117 138.7204 164.2523 > Red. masses -- 1.0475 3.3764 5.3678 > Frc consts -- .0008 .0383 .0853 > IR Inten -- .0139 2.1122 5.4316 > Raman Activ -- .1246 1.7291 .0713 > Depolar -- .7372 .7499 .7106 > Atom AN X Y Z X Y Z X Y Z > 1 6 .00 .00 -.04 .00 .00 .26 .00 >>.00 .07 > 2 7 .00 .00 .03 .00 .00 -.12 .00 .00 >-.13 > 3 6 .00 .00 .00 .00 .00 -.10 .00 >>.00 .19 > 4 1 .00 .00 .01 .00 .00 -.11 .00 >>.00 .39 > 5 7 .00 .00 -.01 .00 .00 -.08 .00 >>.00 .21 > 6 6 .00 .00 -.01 .00 .00 -.06 .00 .00 >-.07 > 7 6 .00 .00 -.02 .00 .00 .17 .00 .00 >-.08 > 8 7 .00 .00 -.01 .00 .00 .20 .00 .00 >-.07 > 9 6 .00 .00 .01 .00 .00 .00 .00 .00 >-.05 > 10 7 .00 .00 .02 .00 .00 -.11 .00 .00 >-.28 > 11 6 .00 .00 .01 .00 .00 -.11 .00 .00 >-.23 > 12 7 .00 .00 .02 .00 .01 -.10 -.01 >-.01 .32 > 13 1 .00 .00 .01 .00 -.03 -.01 .06 >>.02 .51 > 14 1 .00 .00 .03 .00 -.03 -.25 .06 >>.02 .39 > 15 1 .00 .00 -.03 .00 .00 .33 .00 .00 >-.05 > 16 1 .44 .19 -.36 .23 -.16 .26 .09 >-.08 .09 > 17 1 -.47 -.21 -.29 -.25 .17 .28 -.10 >>.09 .09 > 18 1 .03 .02 .54 .02 -.01 .54 .01 >-.01 .17 > 4 5 6 > ?A ?A ?A > Frequencies -- 233.0433 280.7473 386.2434 >>.............. > >-- >Vlad Cojocaru >Max Planck Institut for Biophysical Chemistry >Deparment: 060 >Am Fassberg 11, 37077 Goettingen, Germany >tel: ++49-551-201.1389 >e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de > > > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Thu Aug 29 10:41:19 2002 Received: from mailrelay1.lrz-muenchen.de ([129.187.254.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7TEfJr01207 for ; Thu, 29 Aug 2002 10:41:19 -0400 Received: from [141.84.255.217] by mailout.lrz-muenchen.de with ESMTP for chemistry@ccl.net; Thu, 29 Aug 2002 16:41:15 +0200 Sender: dsmith@cup.uni-muenchen.de Message-Id: <3D6E32A6.462E4C45@cup.uni-muenchen.de> Date: Thu, 29 Aug 2002 16:41:42 +0200 From: David Smith X-Mailer: Mozilla 4.75 [en] (X11; U; OSF1 V5.1 alpha) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: AIMPAC Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all, I was interested in using the AIMPAC program from Bader's research group at McMaster University. I downloaded the source and managed to compile a few of the modules (cubev, gridv, proaimv) but all of the others (bubble, contor, grdvec, profil, releif, and schuss) failed. Has anybody had any experience with this compilation ? Anybody might have suggestions for compiler options that might help ?? I am using Redhat 7.3. Thanks all. --------------------------------------- Dr. David Smith Department of Chemistry Ludwig Maximilians University Butenandt-Str. 5-13, D-81377 Munich Germany Tel.: +49 (0)89 2180 7740 Fax.: +49 (0)89 2180 7738 e-mail: David.Smith@cup.uni-muenchen.de --------------------------------------- From chemistry-request@server.ccl.net Thu Aug 29 12:33:37 2002 Received: from ws0e.pc.chemie.tu-darmstadt.de ([130.83.242.14]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7TGXar06068 for ; Thu, 29 Aug 2002 12:33:36 -0400 Received: from localhost (hatice@localhost) by ws0e.pc.chemie.tu-darmstadt.de (SGI-8.9.3/8.9.3) with ESMTP id SAA21988 for ; Thu, 29 Aug 2002 18:33:31 +0200 (CDT) Date: Thu, 29 Aug 2002 18:33:30 +0200 From: "Dr. Hatice Can" To: chemistry@ccl.net Subject: SUMMARY:CASSCF: StateAverage calculation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, I am summarising the responses those were sent to me for my following question.The question: I am doing CASSCF calculations on a cation. I am not clear about why state average calculations is done. What for is it? Is it really necessary? If you would sent any suggestions or literature name, I will be glad. Responses: Tomasz Borowski ; Thu, 29 Aug 2002 03:21:37 -0400 Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 17kJXz-0008Em-00; Thu, 29 Aug 2002 07:16:55 +0000 Date: Thu, 29 Aug 2002 07:16:55 +0000 (GMT) From: Szilveszter Juhos To: "Ibrahim M.Moustafa" cc: chemistry@ccl.net Subject: Re: CCL:Docking and binding affinity In-Reply-To: <5.1.1.6.0.20020828182638.00a4f548@bute.st-andrews.ac.uk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 28 Aug 2002, Ibrahim M.Moustafa wrote: > Is there any correlation between the binding constant, Ki, of the > ligand and the ability of the docking program to predict its interaction > with the binding site? Well, short answer is no, the long answer is a long-long debate. In general, scoring functions have nothing to do with solvation (though PMF claims to inherently include solvation). Apart from solvation there are other interactions that are not considered or poorly implemented, or are different in a target family than in a the trainig/validation set. Other pain is the entropy loss that you can only guess. The whole business is even worse when it is about weak binders. I would say: scores are more related to some probability that the ligand will bind to the target. With clever pre/post-filtering you can have feasible results for virtual screening, but its relation to dG is, well, debatable. Cheers: Szilva From chemistry-request@server.ccl.net Thu Aug 29 10:46:36 2002 Received: from web21105.mail.yahoo.com ([216.136.227.107]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g7TEkZr01449 for ; Thu, 29 Aug 2002 10:46:36 -0400 Message-ID: <20020829144351.51133.qmail@web21105.mail.yahoo.com> Received: from [193.205.210.2] by web21105.mail.yahoo.com via HTTP; Thu, 29 Aug 2002 16:43:51 CEST Date: Thu, 29 Aug 2002 16:43:51 +0200 (CEST) From: =?iso-8859-1?q?Michele=20Lunelli?= Subject: MOPAC and spin density To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi all, how is calculated in MOPAC the unpaired spin density for odd electron systems, performing ROHF calculation (i.e., using the ESR keyword)? I assume it is calculated as described in Medrano et al., J. Phys. B, 26, 827-833 (1993). Is this correct? Thanks in advance, Michele Lunelli ______________________________________________________________________ Yahoo! Musica: notizie, recensioni, classifiche, speciali multimediali http://it.yahoo.com/mail_it/foot/?http://it.music.yahoo.com/ From chemistry-request@server.ccl.net Thu Aug 29 19:40:13 2002 Received: from travelers.mail.cornell.edu ([132.236.56.13]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g7TNeDr21713 for ; Thu, 29 Aug 2002 19:40:13 -0400 Received: from travelers.mail.cornell.edu (travelers.mail.cornell.edu [132.236.56.13]) by travelers.mail.cornell.edu (8.9.3/8.9.3) with SMTP id TAA20811; Thu, 29 Aug 2002 19:40:11 -0400 (EDT) Date: Thu, 29 Aug 2002 19:40:11 -0400 (EDT) From: rlw28@cornell.edu X-Sender: rlw28@travelers.mail.cornell.edu To: chemistry@ccl.net cc: rlw28@cornell.edu Subject: When is 14 less than 13? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all I have another strange problem. I'm running a PBC simulation in CHARMM. It crashes and I get the following error message: ***** LEVEL 0 WARNING FROM ***** ***** CUTNB is larger than CUTIM: List incomplete. ****************************************** BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS -5 Yet, in my input file as shown below DYNA START VERLET NSTEP 40000 TIMESTEP 0.001 IHBFRQ 10 - IPRFRQ 1000 IHTFRQ 100 IEQFRQ 0 NTRFRQ 0 NSAVC 100 ISEED 314159 - NSAVV 0 FIRSTT 100 FINALT 300 IUNCRD 21 IUNREAD 23 CDIE EPS 1.0 GROUP SWITCH - IUNWRI 20 ISVFRQ 1000 INBFRQ 20 TEMINC 0.5 CUTNB 13.0 CTOFNB 12.0 CTONNB 10.0 - TWINDL -3.0 TWINDH 3.0 IASORS 1 IASVEL 1 ICHECW 1 VSWITCH IPRFRQ 1000 - cutim 14.0 imgfrq 5 you can CLEARLT see that CUTNB (13.0) is LESS than CUTIM (14.0), and not LARGER. What gives???? Richard