From chemistry-request@server.ccl.net Tue Jan 28 05:35:53 2003 Received: from shiva.jussieu.fr ([134.157.0.129]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0SAYdP29951 for ; Tue, 28 Jan 2003 05:34:41 -0500 Received: from as2100.itodys.jussieu.fr (as2100.itodys.jussieu.fr [134.157.24.23]) by shiva.jussieu.fr (8.12.5/jtpda-5.4) with SMTP id h0SAY2YY005931 for ; Tue, 28 Jan 2003 11:34:07 +0100 (CET) Date: Tue, 28 Jan 2003 11:34:01 +0100 Message-Id: <03012811340189@itodys.jussieu.fr> From: petitjean@itodys.jussieu.fr To: chemistry@ccl.net Subject: CCL:molecular modeling freewares X-VMS-To: SMTP%"chemistry@ccl.net" X-Antivirus: scanned by sophie at shiva.jussieu.fr /* Apologize for duplicates */ The following molecular modeling freewares: ARMS, ASV, CSR, DOG, POP, QCM, RADI, are now downloadable from my web site: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html Michel Petitjean, Email: petitjean@itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean@ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html From chemistry-request@server.ccl.net Tue Jan 28 04:59:21 2003 Received: from solar.pharma.hr ([161.53.121.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0S9xIP29532 for ; Tue, 28 Jan 2003 04:59:21 -0500 Received: from 127.0.0.1 (localhost [127.0.0.1]) by dummy.domain.name (Postfix) with SMTP id C42ADC5D7E; Tue, 28 Jan 2003 10:47:34 +0100 (CET) Received: from bf7 (bf7.pharma.hr [161.53.121.47]) by solar.pharma.hr (Postfix) with SMTP id 5AE0DC54DD; Tue, 28 Jan 2003 10:47:34 +0100 (CET) Message-ID: <002301c2c6b4$b8923e00$2f7935a1@pharma.hr> From: "vgomzi" To: Cc: Subject: G98 CCD calculation problem Date: Tue, 28 Jan 2003 11:05:01 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-2" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Dear Sir/Ms, I've been trying to cope with CCD (I'd prefer CCSD(T), though) SP calculation of a complex of cytosine molecules with coordinated Cu-atom. With different ammount of effort, the calculation seems to work fine using HF,MP2,B3LYP methods. But CCD calculation always ends with "File extend in NtrExt1 failed; probably out of disk space." - G98W error, as can be seen from the (relevant) job output quoted below. My question is what should be done and is there some known bug in version of G98 that I use that causes this error message. Please also pay attention that "Estimate disk for full transformation 716426252 words" and, in same section "Total= 1704534156" MaxDsk= 1905032704?! If anyone could further explain what could be the reason for this behaviour, and what should I do to prevent this error, I would appreciate it very much! Thank You very much in advance! Sincerely, Vjeran Gomzi, PhD student Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, CROATIA beginning of output quote ------------------------------------------ ********************************************** Gaussian 98: x86-Win32-G98RevA.11 25-Sep-2001 28-Jan-2003 ********************************************** %Mem=30000000 %chk=tccu-a1-ccd Default route: MaxDisk=6200000000 ------------------------------------------------------ #SP ccd 3-21G Geom=checkpoint Guess=read Prop=EPR TEST ------------------------------------------------------ 1/29=2,38=1/1; 2/40=1/2; 3/5=5,11=9,25=1,30=1/1,2,3; 4/5=1/1; 5/5=2/2; 8/6=6,9=120000,10=1,27=1905032704/1,4; 9/5=6,27=1905032704/13; 6/7=2,8=2,9=2,10=2,17=2,26=4/1,2; 99/5=1,9=1/99; ---------------------------------------------------------------------- Tiocitozin-Cu 2MOLEKULE+Cu-atom SP racun (geometrija iz tccu-a1.chk tj . rezultata tccu-a1.gjf) ---------------------------------------------------------------------- Redundant internal coordinates taken from checkpoint file: tccu-a1-ccd.chk Charge = 1 Multiplicity = 1 Cu,0,-0.7545456806,0.2679000728,0.4224585576 etc ... ................................................................... ... Isotopes: Cu-63,N-14,C-12,O-16,N-14, C-12,N-14,C-12,C-12,H-1,H-1,H-1,H-1,N-14,C-1 2,O-16,N-14,C-12,N-14,C-12,C-12,H-1,H-1,H-1,H-1 Standard basis: 3-21G (6D, 7F) There are 189 symmetry adapted basis functions of A symmetry. Crude estimate of integral set expansion from redundant integrals=1.000. Integral buffers will be 262144 words long. Raffenetti 1 integral format. Two-electron integral symmetry is turned on. 189 basis functions 321 primitive gaussians 71 alpha electrons 71 beta electrons nuclear repulsion energy 1566.9988303827 Hartrees. One-electron integrals computed using PRISM. NBasis= 189 RedAO= T NBF= 189 NBsUse= 189 1.00D-04 NBFU= 189 Initial guess read from the checkpoint file: tccu-a1-ccd.chk Requested convergence on RMS density matrix=1.00D-08 within 64 cycles. Requested convergence on MAX density matrix=1.00D-06. Virtual orbitals will be shifted by 0.200 hartree. SCF Done: E(RHF) = -2410.47713495 A.U. after 1 cycles Convg = 0.2906D-08 -V/T = 2.0037 S**2 = 0.0000 Range of M.O.s used for correlation: 26 189 NBasis= 189 NAE= 71 NBE= 71 NFC= 25 NFV= 0 NROrb= 164 NOA= 46 NOB= 46 NVA= 118 NVB= 118 **** Warning!!: The largest alpha MO coefficient is 0.10598851D+02 Estimate disk for full transformation 716426252 words. Semi-Direct transformation. ModeAB= 4 MOrb= 164 LenV= 29435706 LASXX= 128711270 LTotXX= 153354980 LenRXX= 235554082 LTotAB= 82199102 MaxLAS= 187999350 LenRXY= 0 NonZer= 339621642 LenScr= 517777920 LnRSAI= 373719920 LnScr1= 575139840 LExtra= 2342394 Total= 1704534156 MaxDsk= 1905032704 SrtSym= T ITran= 5 File extend in NtrExt1 failed; probably out of disk space. end of output quote ----------------------------------------------------- From chemistry-request@server.ccl.net Tue Jan 28 01:06:48 2003 Received: from shardagate2.mahindrabt.com ([203.124.158.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0S66kP13730 for ; Tue, 28 Jan 2003 01:06:46 -0500 Received: from thisdomain (mailscan.sharda.mahindrabt.com [10.5.0.97]) by shardagate2.mahindrabt.com (8.9.3/8.9.3/SuSE Linux 8.9.3-0.1) with ESMTP id LAA30131 for ; Tue, 28 Jan 2003 11:36:38 +0530 Received: from intranet.sharda.mahindrabt.com by mahindrabt.com ; Tue, 28 Jan 2003 11:25:26 +0530 Date: Tue, 28 Jan 2003 11:25:26 +0530 X-Originating-IP: 10.5.0.15 X-Auth-User: vijayp@mahindrabt.com Received: from vijayp ([10.5.12.206]) by intranet.sharda.mahindrabt.com (8.9.3/8.9.3) with SMTP id LAA09130; Tue, 28 Jan 2003 11:36:29 +0530 Message-ID: <003301c2c692$a8804a60$ce0c050a@mahindrabt.com> From: "Vijay Pargaonkar" To: , References: Subject: Re: CCL:Industrial Fluid Properties Simulation Challenge Date: Tue, 28 Jan 2003 11:31:07 +0530 MIME-Version: 1.0 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Dear All, First of all, I would like to appreciate the efforts put up till now for simulating thermophysical properties simulation. Diffusion coefficient and thermal diffussion coefficient can be considered as good challenge. Diffussion coefficient(DC) governs mass transfer across concentration gradient. Thermal diffussion coefficient (TDC) governs mass transfer across temperature gradient(SORET effect). Both these properties are crucial for fluid dynamic simulations. Also there (DC as well as TDC) dependance is strong on temperature and molecular weight. Thermal diffussion coefficient depends on temperature, molecular weight of species and the mole fractions of the species involved in the simulation. Many times these chemicals are costlier, making their properties as good candidates for simulation. Theory of gases provides a way out for estimating the above described properties based on the fluids critical point and boiling point. However, these estimatiomns vary 10% to 15% from the real values. This results in wrong simulation of fluid flow modelling. Applicability of the property TDC is crucial especially if, mixture consists of fluids with a lot of difference in their molecular weights and when temperature variations are more in the domain of interest. There are various application areas in industry where such cases arise. Carrying out experiements for finding out TDC for gases is neither easy nor cheap. Hence, simulations are must. I hope an accurate estimation/simulation of these properties will help a lot in getting correct insight of many fluid flow simulations involving different chemicals. With warm regards Pargaonkar Vijay ********************************************************* Disclaimer This message (including any attachments) contains confidential information intended for a specific individual and purpose, and is protected by law. If you are not the intended recipient, you should delete this message and are hereby notified that any disclosure, copying, or distribution of this message, or the taking of any action based on it, is strictly prohibited. ********************************************************* Visit us at http://www.mahindrabt.com From chemistry-request@server.ccl.net Tue Jan 28 07:26:59 2003 Received: from axovansrv.axovan.com ([213.189.136.190]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0SCQvP31720 for ; Tue, 28 Jan 2003 07:26:58 -0500 Received: by AXOVANSRV with Internet Mail Service (5.5.2653.19) id ; Tue, 28 Jan 2003 13:26:57 +0100 Message-ID: <97DDDA51F4F8D411AC140050DA60DC202E3DF4@AXOVANSRV> From: Korff Modest To: "'CHEMISTRY@ccl.net'" Subject: RE: CCL:request information on Genetic Algorithms source code and applications Date: Tue, 28 Jan 2003 13:26:54 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" For an implementation of code try the genetic algorithm library GALIB http://lancet.mit.edu/ga/ from M. Wall at the MIT. It is a C++ library with an outstanding design. The code is very good documented. So it is very convenient to adapt the code to your own needs. For genetic algorithms in chemistry have a view at: http://panizzi.shef.ac.uk/cisrg/links/ea_bib.html and http://citeseer.nj.nec.com/317688.html Kind regards modest From chemistry-request@server.ccl.net Tue Jan 28 04:45:33 2003 Received: from jubilantbiosys.com ([202.144.86.69]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0S9jUP29342 for ; Tue, 28 Jan 2003 04:45:31 -0500 Received: from ramya ( [192.168.1.75] (may be forged)) (authenticated) by jubilantbiosys.com (8.11.6/8.11.6) with ESMTP id h0S9nue20636 for ; Tue, 28 Jan 2003 15:19:56 +0530 Message-ID: <006401c2c6b1$80f1da80$4b01a8c0@jubilant.local> From: "Ramya" To: Subject: CCL: Hydrogen bond acceptors Date: Tue, 28 Jan 2003 15:11:41 +0530 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0061_01C2C6DF.8FB5FAF0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6700 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 This is a multi-part message in MIME format. ------=_NextPart_000_0061_01C2C6DF.8FB5FAF0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Hi, In small molecules, can we consider halogens as hydrogen bond = acceptors? And along similar lines, Is sulphur treated as a hydrogen bond acceptor? Expecting reply, Ramya ------=_NextPart_000_0061_01C2C6DF.8FB5FAF0 Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable
Hi,
    In small molecules, = can we=20 consider halogens as hydrogen bond acceptors?
 
And along similar lines, Is sulphur = treated as a=20 hydrogen bond acceptor?
 
Expecting reply,
Ramya
------=_NextPart_000_0061_01C2C6DF.8FB5FAF0-- From chemistry-request@server.ccl.net Tue Jan 28 05:16:46 2003 Received: from jubilantbiosys.com ([202.144.86.69]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0SAGdP29715 for ; Tue, 28 Jan 2003 05:16:42 -0500 Received: from ramya ( [192.168.1.75] (may be forged)) (authenticated) by jubilantbiosys.com (8.11.6/8.11.6) with ESMTP id h0SAL8e21283 for ; Tue, 28 Jan 2003 15:51:08 +0530 Message-ID: <007f01c2c6b5$dcc196d0$4b01a8c0@jubilant.local> From: "Ramya" To: Subject: CCL: Proximity of N and O Date: Tue, 28 Jan 2003 15:42:53 +0530 MIME-Version: 1.0 Content-Type: multipart/related; boundary="----=_NextPart_000_0079_01C2C6E3.EC1266E0"; type="multipart/alternative" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6700 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 This is a multi-part message in MIME format. ------=_NextPart_000_0079_01C2C6E3.EC1266E0 Content-Type: multipart/alternative; boundary="----=_NextPart_001_007A_01C2C6E3.EC188160" ------=_NextPart_001_007A_01C2C6E3.EC188160 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable =20 Hi,=20 I have a problem identifying the proximity of N with O in the = above molecule. Basically i want the count of N-C-O 's ("-" represents that the atoms = are bonded, bond type is immaterial, whether single or double) in the = above molecule.=20 Is the count =3D 2 or 3? The same N is accounted for in 2 situations( red and brown) and the same = O & C are accounted for in 2 situations (red and blue)=20 Is that overlap counted? Ramya ------=_NextPart_001_007A_01C2C6E3.EC188160 Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable
          &nbs= p;            = ;     =20

 

Hi,=20
     =20 I have a problem identifying the proximity of N with O in the above=20 molecule.
Basically=20 i want the count of N-C-O 's ("-" represents that the atoms are bonded, = bond=20 type is immaterial, whether single or double) in the above molecule.=20
 
Is=20 the count =3D 2 or 3?
 
The=20 same N is accounted for in 2 situations( red and brown) and the same=20 O & C are accounted for in 2 situations (red and blue)=20
Is=20 that overlap counted?
 
Ramya
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------=_NextPart_000_0079_01C2C6E3.EC1266E0-- From chemistry-request@server.ccl.net Tue Jan 28 03:48:57 2003 Received: from mailstudenti.unimi.it ([159.149.10.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0S8muP15993 for ; Tue, 28 Jan 2003 03:48:57 -0500 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailstudenti.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0H9F004DO1LE6H@mailstudenti.unimi.it> for chemistry@ccl.net; Tue, 28 Jan 2003 09:44:03 +0100 (MET) Received: from heisenberg (heisenberg.chimica.unimi.it [159.149.240.30]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0H9F008D11LFMM@smtp.unimi.it> for chemistry@ccl.net; Tue, 28 Jan 2003 09:44:03 +0100 (MET) Date: Tue, 28 Jan 2003 09:47:51 +0100 From: Alessandro Contini Subject: Re: CCL:Intramolecular hydrogen bond In-reply-to: <006f01c2c5c7$f8d026f0$4b01a8c0@jubilant.local> To: Ramya Cc: CCL Message-id: <200301280947.51124.alessandro.contini@unimi.it> Organization: Istituto di Chimica Organica "Alessandro Marchesini" MIME-version: 1.0 Content-type: text/plain; charset=windows-1252 User-Agent: KMail/1.4.3 References: <006f01c2c5c7$f8d026f0$4b01a8c0@jubilant.local> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h0S8mvP15994 Hi, there are some packages that display H bonds, here are some of them. MOLDEN http://www.caos.kun.nl/~schaft/molden/CopyRight.html AUTODOCK TOOLS http://www.scripps.edu/pub/olson-web/dock/autodock/ MOLEKEL http://www.cscs.ch/molekel/ SWISS-PDB VIEWER http://www.expasy.org/spdbv/ Those packages are able to read PDB file formats and to calculate H-bonds. Hope this help Alessandro Alle 06:50, lunedì 27 gennaio 2003, Ramya ha scritto: > Hi, > How to identify the presence of intramolecular hydrogen bonds in a > given molecule? If someone can help me out with this, it will be great..... > Thanks in advance, > Ramya -- Dott. Alessandro Contini Istituto di Chimica Organica "Alessandro Marchesini" Facoltà di Farmacia Università degli Studi di Milano Via Venezian, 21 20133 Milano Tel. +390250314480 Fax +390250314476 http://users.unimi.it/istchimorg/pagconthtm.htm From chemistry-request@server.ccl.net Tue Jan 28 09:57:54 2003 Received: from kdmail2.netcologne.de ([194.8.194.86]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0SEvsP02753 for ; Tue, 28 Jan 2003 09:57:54 -0500 Received: from cosmologic.de (xdsl-195-14-220-124.netcologne.de [195.14.220.124]) by kdmail2.netcologne.de (Mirapoint Messaging Server MOS 2.9.3.5) with ESMTP id AAG31940 (AUTH klamt@cosmologic.de); Tue, 28 Jan 2003 15:57:38 +0100 (CET) Message-ID: <3E369A5E.7070705@cosmologic.de> Date: Tue, 28 Jan 2003 15:57:34 +0100 From: "Dr. Andreas Klamt" Organization: COSMOlogic GmbH&CoKG User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en,pdf MIME-Version: 1.0 CC: chemistry@ccl.net Subject: Re: CCL:Industrial Fluid Properties Simulation Challenge References: <003301c2c692$a8804a60$ce0c050a@mahindrabt.com> Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit Dear All, Seeing the discussion about the challenge, I think that the winners of the First Industrial Fluid Properties Simulation Challenge should once be announced to the CCL. Since nobody else does it, I have to do it myself: part 1: The most accurate prediction of vapor liquid equilibria for mixtures of dimethyl ether/propylene and of nitroethane/propylene glycol was obtained by Andreas Klamt and Frank Eckert from COSMOLogic GmbH&CoKG. (See http://www.cosmologic.de/SimulationChallenge.pdf) part 2: The winner of the density prediction section was Huai Sun from Aeon Technology in San Diego. part 3: The champions in the viscosity prediction for n-nonane/isopropanol mixtures were Marcus Martin and Aidan Thompson from Sandia. Andreas -------------------------------------------------------------------------------- Dr. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: 49-2171-73168-1 Fax: ...-9 e-mail: andreas.klamt@cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Tue Jan 28 10:22:42 2003 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0SFMgP03327 for ; Tue, 28 Jan 2003 10:22:42 -0500 Received: from cornell.edu ([66.69.81.224]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id KAA20858; Tue, 28 Jan 2003 10:22:42 -0500 (EST) Message-ID: <3E36A03D.65C0106E@cornell.edu> Date: Tue, 28 Jan 2003 09:22:38 -0600 From: "Dr. Richard L. Wood" Organization: Cornell University X-Mailer: Mozilla 4.5 [en]C-CCK-MCD {TLC;RETAIL} (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Re: missing bonds in Rasmol Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all Thanks to Warren Delano, Tim R,. Jim Kress, Steve Williams, Mark, Anthony Lewis, Nikolaus Stiefl, and Ben Carrington for their helpful suggestions. What I've done is to use BabelWin to convert my xyz file to a pdb file which has the connectivity table at the end, and Rasmol is able to read this file with all the bonds. The version of Rasmol that works with Chem2Pac gives a nice clean, easily resizable image that can be copy pasted into a Word doc, as opposed to saving images as bitmaps. Now if I can just figure out a way to convert all my CHARMm files that have missing bonds in Rasmol (Rasmol has a problem with a glycosidic linkage, I think) to pdb files (BabelWin won't handle CHARMm files), then I'll be all set... Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Department of Chemistry Trinity University, San Antonio, TX 78212 From chemistry-request@server.ccl.net Tue Jan 28 20:30:08 2003 Received: from sciences.sdsu.edu ([130.191.226.112]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0T1U5P14022 for ; Tue, 28 Jan 2003 20:30:08 -0500 Received: from localhost (jcuervo@localhost) by sciences.sdsu.edu (8.10.2+Sun/8.8.8/SCEC-8.8.8-AS.AR.S5) with ESMTP id h0T1U3v00152 for ; Tue, 28 Jan 2003 17:30:03 -0800 (PST) Date: Tue, 28 Jan 2003 17:30:03 -0800 (PST) From: Javier Cuervo To: chemistry@ccl.net Subject: protein-protein Dissociation Constant SUMARY In-Reply-To: <1097.132.178.216.35.1042818761.squirrel@webmail.velocitus.net> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Thank you for the information given, has being really helpful, here is the sumary from:lwarner@velocitus.net No databases that I am aware of, but PubMed is a good resource for journal articles that may be of help. http://www.ncbi.nlm.nih.gov/PubMed/ from:james.metz@abbott.com Javier, I am not aware of any databases of protein-protein dissociation constants either. First, take a look at the article, Horton, N. and Lewis, M. Protein Sci (1992) 1, 169, which describes the development of a semi-empirical, fast method to calculate Kd's for protein - protein complexes based on atomic solvation parameters, accessible surface areas, etc. I think there were a decent number of experimentally determined Kd's listed somewhere in the paper. Second, not to self-promote, but you might also want to get a copy of my Ph.D. thesis (Purdue Univ., Chem. Dept, 1991). In collaboration with Eli Lillly and Company, I used AMBER FEP methodology to calculate the relative self-association free energies of several insulin analogues using various thermodynamic cycles involving insulin monomers and dimers. I never published this work, because I couldn't get the relative numbers to tightly agree with experiment, but I did correctly predict the trends in self-association for 5 different insulin complexes. The Ph.D. thesis does contain a table or two with experimentally determined Kd data from analytical ultracentrifugation measurements. Third, you might want to consider the program PLOGP from the Institute of Physical Chemistry, Peking (contact Gao Ying at gao@mdl.ipc.pku.edu.cn). Primary literature reference is : Tao, P et al. J. Mol. Model. (1999) 5, 189. This very interesting program calculates logP values for peptides and even entire proteins, and you can visualize the molecular lipophilicity as a contour map, etc. Regards, Jim Metz Javier Cuervo Graduate Student Computational Science Research Center SDSU From chemistry-request@server.ccl.net Tue Jan 28 13:56:20 2003 Received: from dire.bris.ac.uk ([137.222.10.60]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0SIuKP07878 for ; Tue, 28 Jan 2003 13:56:20 -0500 Received: from sis.bris.ac.uk by dire.bris.ac.uk with SMTP-PRIV with ESMTP; Tue, 28 Jan 2003 18:56:09 +0000 Received: from simpson (simpson.chm.bris.ac.uk [137.222.42.59]) by sis.bris.ac.uk (8.11.6/8.11.6) with SMTP id h0SItRT17239 for ; Tue, 28 Jan 2003 18:55:27 GMT Message-ID: <004a01c2c6ff$ee5197c0$3b2ade89@chm.bris.ac.uk> From: Chris Arthur To: CHEMISTRY Subject: Autodock on Linux Date: Tue, 28 Jan 2003 19:03:23 -0000 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0047_01C2C6FF.EE23D100" 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 This is a multi-part message in MIME format. ------=_NextPart_000_0047_01C2C6FF.EE23D100 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi guys I was wondering if anyone had seen this error before (I've just compiled = autodock on Red Hat 8 and its been doing strange things) I run=20 > mol2topdbqs molecule.mol2 (where molecule is molecule = name) and get > awk: /mol2fftopdbq.awk:90:fatal:expression for '<' reduction has null = string value Anyone have any ideas? Thanks in advance Chris ------=_NextPart_000_0047_01C2C6FF.EE23D100 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi guys
 
I was wondering if anyone had seen this = error=20 before (I've just compiled autodock on Red Hat 8 and its been doing = strange=20 things)
 
I run
> mol2topdbqs=20 molecule.mol2          =        =20 (where molecule is molecule name)
and get
> awk: = /mol2fftopdbq.awk:90:fatal:expression for=20 '<' reduction has null string value
 
Anyone have any ideas?
 
Thanks in advance
 
Chris
------=_NextPart_000_0047_01C2C6FF.EE23D100-- From chemistry-request@server.ccl.net Tue Jan 28 14:56:35 2003 Received: from viper.abbott.com ([130.36.44.77]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0SJuZP08904 for ; Tue, 28 Jan 2003 14:56:35 -0500 Received: from abtmr1.abbott.com (abtmr1.abbott.com [10.254.245.1]) by viper.abbott.com (Switch-2.1.4/Switch-2.1.0) with ESMTP id h0SJujY19831 for ; Tue, 28 Jan 2003 13:56:45 -0600 (CST) Received: from abtapn561.northamerica.intra.abbott.com (localhost [127.0.0.1]) by abtmr1.abbott.com (Switch-2.0.6/Switch-2.0.6) with ESMTP id h0SJuZi11093 for ; Tue, 28 Jan 2003 13:56:35 -0600 (CST) To: chemistry@ccl.net Cc: james.metz@abbott.com Subject: CCL: X-ray or NMR structures of weakly bound complexes X-Mailer: Lotus Notes Release 5.0.5 September 22, 2000 Message-ID: From: james.metz@abbott.com Date: Tue, 28 Jan 2003 13:55:46 -0600 X-MIMETrack: Serialize by Router on ABTAPN561/ESVR/ABBOTT(Release 5.0.5 |September 22, 2000) at 01/28/2003 01:52:18 PM, Serialize complete at 01/28/2003 01:52:18 PM MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="=_alternative 006D8AF386256CBC_=" This is a multipart message in MIME format. --=_alternative 006D8AF386256CBC_= Content-Type: text/plain; charset="us-ascii" CCL, I am looking for X-ray or NMR structures of weakly bound ligands (Ki > 50 uM) to proteins. The structures should include ordered water. I am aware of several structures of weakly bound ligands in the PDB e.g., benzene bound to lysozyme (PDB code 1l83, pKi = 3.4), 3-phenylpropylamine bound to trypsin (PDB code 1tnk, pKi = 1.49), etc. I have also searched the the Binding DB (http://www.bindingdb.org/bind/index.jsp), but there are 0 examples of ligands which meet this criteria. Can anyone help with references, structures, etc? Thank you, Jim Metz James T. Metz, Ph.D. Research Investigator Chemist GPRD R46Y AP10-2 Abbott Laboratories 100 Abbott Park Road Abbott Park, IL 60064-6100 U.S.A. Office (847) 936 - 0441 FAX (847) 935 - 0548 james.metz@abbott.com --=_alternative 006D8AF386256CBC_= Content-Type: text/html; charset="us-ascii"
CCL,

        I am looking for X-ray or NMR structures of weakly bound ligands (Ki > 50 uM) to proteins.  The structures should include ordered
water.

        I am aware of several structures of weakly bound ligands in the PDB e.g., benzene bound to lysozyme (PDB code 1l83, pKi = 3.4),
3-phenylpropylamine bound to trypsin (PDB code 1tnk, pKi  = 1.49), etc.  I have also searched the the Binding DB (http://www.bindingdb.org/bind/index.jsp), but there are 0 examples of ligands which meet this criteria.

        Can anyone help with references, structures, etc?

        Thank you,
        Jim Metz

James T. Metz, Ph.D.
Research Investigator Chemist

GPRD R46Y AP10-2
Abbott Laboratories
100 Abbott Park Road
Abbott Park, IL  60064-6100
U.S.A.

Office (847) 936 - 0441
FAX    (847) 935 - 0548

james.metz@abbott.com
 --=_alternative 006D8AF386256CBC_=-- From chemistry-request@server.ccl.net Tue Jan 28 15:21:59 2003 Received: from zeus.biomol.uci.edu ([128.195.179.142]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h0SKLwP09251 for ; Tue, 28 Jan 2003 15:21:58 -0500 Received: from uci.edu (heffron@athena.biomol.uci.edu [128.195.179.141]) by zeus.biomol.uci.edu (8.9.3/) with ESMTP id UAA1547160; Tue, 28 Jan 2003 20:21:56 GMT Sender: heffron@uci.edu Message-ID: <3E36E664.1EFF4E15@uci.edu> Date: Tue, 28 Jan 2003 12:21:56 -0800 From: Susan Heffron Reply-To: sheffron@uci.edu Organization: UCI X-Mailer: Mozilla 4.78C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Michele Porro CC: chemistry@ccl.net Subject: Re: CCL:AutoDock Tools+charges (2nd response) References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi again, Mike. It just occurred to me that if you're using autodock tools, you just need to provide Rij and epsij when it asks for them. I believe the values needed are the ones listed for Calcium-Calcium in the (long) list that I previously sent. So, that would be: rij = 1.98 epsij= 0.550 * 0.1485 = 0.081675 Best regards, Susan Michele Porro wrote: > > Dear CCL, i'm an "Autodock beginner" and i have the two following questions: > > 1) By reading my macromolecule in AutoDock Tools i become the message "not > integral charge on residue..." what does it mean and which charges are > suitable for working with Autodock? Does ADT accept only formal charges? > > 2) My macromolecule contains Ca2+, i set Ca2+ = M but i'm still looking > for good Ca2+ parameters, have anyone of you good suggestion? > How do i correct edit the "Ca-line" in my pdb-file? > > I'll summarize. > Thank you all in advance > Have a nice weekend > bye mike > > ******************************** > Michele Porro > Institute of Molecular Pharmacy > Pharmacenter > University of Basel > Klingelbergstrasse 50 > CH-4056 Basel > > Phone : +41 61 267 15 63 > FAX : +41 61 267 15 52 > e-mail: michele.porro@unibas.ch > > http://www.pharma.unibas.ch > http://www.pharmacenter.ch > ******************************** > > > -= 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 -- ------------------------------------------------------------------ Susan Heffron Dept. of Physiology and Biophysics University of California, Irvine Irvine, CA 92697-4560 U.S.A. phone: (949) 824-4625 FAX: (949) 824-8540 ------------------------------------------------------------------