From chemistry-request@server.ccl.net Mon Mar 25 01:42:06 2002 Received: from gate.boehringer-ingelheim.de ([148.188.1.36]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g2P6g5p18126 for ; Mon, 25 Mar 2002 01:42:05 -0500 Received: from bibex01.bc.de.bic by gate.boehringer-ingelheim.de via smtpd (for server.ccl.net [192.153.40.39]) with SMTP; 25 Mar 2002 06:39:55 UT Received: by bibex01.eu.boehringer.com with Internet Mail Service (5.5.2653.19) id <1NL3J87S>; Mon, 25 Mar 2002 07:41:56 +0100 Message-ID: From: Christian.Pilger@bc.boehringer-ingelheim.com To: meenatul@bom2.vsnl.net.in Cc: chemistry@ccl.net Subject: AW: Histidine Date: Mon, 25 Mar 2002 07:41:56 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain Dear Meena, the way I do this is to inspect each HIS residue manually and have a look on the surrounding amino acids in terms of ionization state and hydrogen bond donor/acceptor capabilities. In many cases you get a good hint about where to put the proton, especially if you have a GLU or an ASP in hydrogen bonding distance, there is a good chance, that the HIS will form a salt bridge, hence it carries protons on both nitrogens. In analogy you can make a decision to put the proton on N(delta) or N(epsilon) depending on the closeness of HB donors/acceptors. In cases, where I can not make a clear estimate, I arbitrarily put the proton on N(delta). Cheers, Christian ________________________________________________________________ Dr. Christian Pilger Dept. Chemical Research / Structural Research K91-00-10 Boehringer Ingelheim Pharma KG D-88397 Biberach/Germany Phone: 07351-545749 Fax: 07351-5497924 mailto: christian.pilger@bc.boehringer-ingelheim.com From chemistry-request@server.ccl.net Mon Mar 25 03:06:34 2002 Received: from rbadb2.rbacpxclu.bas.roche.com ([196.3.50.241]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2P86Xp19282 for ; Mon, 25 Mar 2002 03:06:33 -0500 Received: from CONVERSION-DAEMON.Roche.COM by Roche.COM (PMDF V6.0-025 #47170) id <01KFRT3TDGBK9D39RW@Roche.COM> for chemistry@ccl.net; Mon, 25 Mar 2002 09:04:13 +0100 Received: from rbamsemcn1.bas.roche.com (rbamsemcn1.bas.roche.com [145.245.211.139]) by Roche.COM (PMDF V6.0-025 #47170) with ESMTP id <01KFRT3SEYZ69C6Z2I@Roche.COM> for chemistry@ccl.net; Mon, 25 Mar 2002 09:04:06 +0100 Received: by rbamsemcn1.bas.roche.com with Internet Mail Service (5.5.2653.19) id ; Mon, 25 Mar 2002 09:05:28 +0100 Content-return: allowed Date: Mon, 25 Mar 2002 09:05:09 +0100 From: "Shapiro, Stuart {Basi~Basel}" Subject: ?s re variables in Stokes-Einstein eqn. To: "'chemistry@ccl.net'" Cc: "'stuart.shapiro@basileapharma.com'" Message-id: MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-type: text/plain; charset=iso-8859-1 Dear Colleagues, In the Stokes-Einstein equation for the diffusion coefficient for spherical molecules, is the radius of the molecule under consideration taken to be the hydrodynamic radius, the radius of gyration, or some other kind of radius? Also, in this equation is the viscosity taken to be the shear viscosity, intrinsic viscosity, kinematic viscosity, or some other kind of viscosity? Along the same lines, if you measure the viscosity of a solution using a Ubbeholde capillary viscometer, are you measuring the kinematic viscosity, the shear viscosity, the relative viscosity, or some other kind of viscosity? Kind address responses to me _directly_ at stuart.shapiro@basileapharma.com Thanks in advance to all responders, S. Shapiro stuart.shapiro@basileapharma.com From chemistry-request@server.ccl.net Mon Mar 25 04:28:30 2002 Received: from cuces.unisi.it ([193.205.4.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2P9SUp21140 for ; Mon, 25 Mar 2002 04:28:30 -0500 Received: from unisi.it (sgio2.ctf.unisi.it [172.16.3.81]) by unisi.it (PMDF V6.0-24 #43309) with ESMTPA id <01KFRW25S3O4005UAW@unisi.it> for chemistry@ccl.net; Mon, 25 Mar 2002 10:28:18 +0100 (MET) Date: Mon, 25 Mar 2002 10:28:13 -0800 From: Stefano Forli Subject: QSAR equations Sender: stefano@unisi.it To: chemistry@ccl.net Message-id: <3C9F6C3D.614F58F5@unisi.it> MIME-version: 1.0 X-Mailer: Mozilla 4.5 [en] (X11; I; IRIX 6.3 IP32) Content-type: text/plain; charset=UTF-7 Content-transfer-encoding: 7BIT X-Accept-Language: en Dear list, I'm working on a pseudoreceptor model, using the PrGen software. I'm writing to ask about QSAR equations, in particular, about the physical meaning of the slope value. It's well to obtain a good correlation with a big value of slope, or not? What is the optimal value? Thanks Stefano -- *********************************** Forli Stefano Dip. Farmaco Chimico Tecnologico Universita' degli Studi di Siena Via Aldo Moro I-53100 Siena, Italy Phone: ++39 0577 234307 Fax: ++39 0577 234333 *********************************** From chemistry-request@server.ccl.net Mon Mar 25 04:45:08 2002 Received: from luc.ac.be ([193.190.2.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2P9j8p21970 for ; Mon, 25 Mar 2002 04:45:08 -0500 Received: from sbg-ts (localhost [127.0.0.1]) by luc.ac.be (8.9.3/8.9.3) with SMTP id KAA30929; Mon, 25 Mar 2002 10:44:58 +0100 (MET) Date: Mon, 25 Mar 2002 10:44:58 +0100 (MET) Message-Id: <200203250944.KAA30929@luc.ac.be> X-Sender: lucp1381@mail.luc.ac.be X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: "Kiniu WONG \(Kin-Yiu\)" , chemistry@ccl.net From: sergiusz kwasniewski Subject: Re: CCL:TDDFT in terms of polarization propagator Hi, I only got one answer: serge, i'm pretty sure this has been done, have a look at the book by simons and jorgenson [second quanitzation in chemistry i think its called?], or some of the work of danny yeager noj -- Dr. N.O.J. Malcolm n.malcolm@umist.ac.uk Chemistry Department UMIST, Sackville Street Manchester, England. M60 1QD I guess this is about the book 'second quantization-based methods in QC' from P Jorgenson and J Simons ? Serge At 07:53 AM 3/7/02 -0500, Kiniu WONG \(Kin-Yiu\) wrote: >----- Original Message ----- >From: "sergiusz kwasniewski" >To: >Sent: Thursday, March 07, 2002 4:17 AM >Subject: CCL:TDDFT in terms of polarization propagator > > >> Hi, >> >> Does someone know whether TDDFT (or TDDFRT) has been derived in terms >> of the polarization propagator (Green's functions). It would easen the >> comparison with standard derivation of RPA (or TDHF). >> >> Thanks, >> >> Serge Kwasniewski ___________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 032 (0)11/268315 fax : 032 (0)11/268301 email : sergiusz.kwasniewski@luc.ac.be http://www.luc.ac.be/Research/TheoChem ___________________________________________________ From chemistry-request@server.ccl.net Mon Mar 25 05:00:40 2002 Received: from cuces.unisi.it ([193.205.4.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2PA0ep22978 for ; Mon, 25 Mar 2002 05:00:40 -0500 Received: from unisi.it (sgio2.ctf.unisi.it [172.16.3.81]) by unisi.it (PMDF V6.0-24 #43309) with ESMTPA id <01KFRX64ZQAQ005T4E@unisi.it> for chemistry@ccl.net; Mon, 25 Mar 2002 11:00:33 +0100 (MET) Date: Mon, 25 Mar 2002 11:00:27 -0800 From: Stefano Forli Subject: QSAR equations: Addendum Sender: stefano@unisi.it To: chemistry@ccl.net Message-id: <3C9F73CB.12F21FE0@unisi.it> MIME-version: 1.0 X-Mailer: Mozilla 4.5 [en] (X11; I; IRIX 6.3 IP32) Content-type: text/plain; charset=UTF-7 Content-transfer-encoding: 7BIT X-Accept-Language: en I would also ask about the intercept value, and its implications in a good correlation... Thanks! S. -- *********************************** Forli Stefano Dip. Farmaco Chimico Tecnologico Universita' degli Studi di Siena Via Aldo Moro I-53100 Siena, Italy Phone: ++39 0577 234307 Fax: ++39 0577 234333 *********************************** From chemistry-request@server.ccl.net Mon Mar 25 08:55:04 2002 Received: from luc.ac.be ([193.190.2.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2PDt4p28425 for ; Mon, 25 Mar 2002 08:55:04 -0500 Received: from sbg-ts (localhost [127.0.0.1]) by luc.ac.be (8.9.3/8.9.3) with SMTP id OAA12115 for ; Mon, 25 Mar 2002 14:54:58 +0100 (MET) Date: Mon, 25 Mar 2002 14:54:58 +0100 (MET) Message-Id: <200203251354.OAA12115@luc.ac.be> X-Sender: lucp1381@mail.luc.ac.be X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@ccl.net From: sergiusz kwasniewski Subject: question on vibronic coupling calculation Hi everyone, I'm trying to write a program to account for vibronic coupling on UV/Visible absorption spectra. For the vibronic progression with only one symmetric vibrational mode and up to 3 quanta, the Frank-Condon approximation is fairly easy to implement. However, if I want to include more vibrational modes, I encounter a small problem: I(lambda) ~ SUM ( PRODUCT ( F.C.'s) * D ) where lambda is given in wavelength (nm), the sum is over the quanta (0-3), and the product over the Frank-Condon factors corresponding to the different vibrational modes. Now: in order to describe the band shape factor D, I have to calculate a factor (lambda - lambda(max))^2. How does this factor change while including more than one vibrational frequency ? What I found is: (lambda - (lambda(max) + SUM nu * omega))^2 where nu is the quantum (which is a constant in this summation) and omega is the energy of the vibration, but then instead of having a series of 6 additional peaks besides your lambda(max) (i.e. 3 per vibrational modes), these modes are coupled now 2 by 2 in order to give 3 additional peaks but with an almost doubled spacing (depending on the energies of the vibrations off course). Does anyone know if this is correct, the literature I found about vibronic coupling doesn't explain this thoroughly. I appreciate any kind of help !! Serge ___________________________________________________ Sergiusz Kwasniewski LUC SBG/TS Universitaire Campus Gebouw D 3590 Diepenbeek BELGIUM tel(direct): 032 (0)11/268315 fax : 032 (0)11/268301 email : sergiusz.kwasniewski@luc.ac.be http://www.luc.ac.be/Research/TheoChem ___________________________________________________ From chemistry-request@server.ccl.net Mon Mar 25 09:50:31 2002 Received: from ns2.tudelft.nl ([130.161.180.65]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2PEoVp30089 for ; Mon, 25 Mar 2002 09:50:31 -0500 Received: from listserv.tudelft.nl (listserv.tudelft.nl [130.161.180.33]) by mailhost1.tudelft.nl (PMDF V6.0-025 #40924) with ESMTP id <0GTJ00J2RAJXBK@mailhost1.tudelft.nl> for chemistry@ccl.net; Mon, 25 Mar 2002 15:50:21 +0100 (MET) Received: from stm-ltc2.dct.tudelft.nl (stm-ltc2.dct.tudelft.nl [130.161.196.198]) by listserv.tudelft.nl (8.10.2+Sun/8.10.2) with ESMTP id g2PEoD519371 for ; Mon, 25 Mar 2002 15:50:21 +0100 (MET) Received: from STM-LTC2/SpoolDir by stm-ltc2.dct.tudelft.nl (Mercury 1.47) ; Mon, 25 Mar 2002 15:50:21 +0000 (MET-1MEST) Received: from SpoolDir by STM-LTC2 (Mercury 1.47); Mon, 25 Mar 2002 15:50:13 +0000 (MET-1MEST) Date: Mon, 25 Mar 2002 15:50:08 +0100 From: Stefan Bromley Subject: GULP with MPI/LAM To: chemistry@ccl.net Message-id: <3C9F472E.1152.A350CEB@localhost> MIME-version: 1.0 X-Mailer: Pegasus Mail for Win32 (v3.12c) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Priority: normal I have been runnning MD jobs with GULP (General Utility Lattice Program) on a 16 node Athlon based Beowulf cluster but have been unable to run consecutive MPI jobs without a remake of the source (just deleting the final source file and remaking - taking a second or two) each time. Although it works, it is a rather unsatisfactory way of working and limits me to one MPI job at a time. It seems that every time GULP finishes it somehow manages to corrupt the LAM MPI libraries, and when a second run of GULP is attempted an error occurs just as the first step is to proceed: ****************************************************************************** Output for configuration 1 * ****************************************************************************** MPI_Recv: process in local group is dead (rank 0, MPI_COMM_WORLD) Rank (0, MPI_COMM_WORLD): Call stack within LAM: Rank (0, MPI_COMM_WORLD): - MPI_Recv() Rank (0, MPI_COMM_WORLD): - MPI_Reduce() Rank (0, MPI_COMM_WORLD): - MPI_Allreduce() Rank (0, MPI_COMM_WORLD): - main() Looking at the source code this seems to be the point in the code where the memory allocation takes place. I have therefore tried all combinations of -DMALLOC and -DF90 in the getmachine setup but none seems to fix the problem. I am using LAM-MPI compiled with the GNU compilers and configured to use the pgf90 compiler under Linux. Has anyone managed to compile a more robust LAM- MPI/pgf90/GULP setup (or similar), or does anyone have any suggestions of how to do so. An mpirun of a consecutive GULP job with np 1 gives no problem only with 2 or more processors. I have also tried using MPICH but I couldn't even run/compile/link GULP sucessfully then. Many thanks for your help in advance. Stefan ________________________________________________________ Dr Stefan T. Bromley Laboratory of Applied Organic Chemistry and Catalysis DelftChemTech, Delft University of Technology Julianalaan 136, 2628 BL Delft The Netherlands Phone : + 31 1527 89418 e-mail : S.T.Bromley@tnw.tudelft.nl ________________________________________________________ From chemistry-request@server.ccl.net Mon Mar 25 18:47:38 2002 Received: from mail4.uts.ohio-state.edu ([128.146.214.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2PNlcp16975 for ; Mon, 25 Mar 2002 18:47:38 -0500 Received: from osu.edu (laba-pc22.pharmacy.ohio-state.edu [128.146.80.238]) by mail4.uts.ohio-state.edu (8.9.3/8.9.3) with ESMTP id SAA22040 for ; Mon, 25 Mar 2002 18:47:32 -0500 (EST) Sender: praveen@mail4.uts.ohio-state.edu Message-ID: <3C9FB714.F54C0047@osu.edu> Date: Mon, 25 Mar 2002 18:47:32 -0500 From: Praveen M Bahadduri X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: AUTODOCK3 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi! I am using autodock3 for sometime. I went through the dockings a couple of times. But when I read the ligand.macro.dlg.pdb in the sybyl window, It just gives me different positions of the ligand molecule with the macromolecule missing in the background. Anybody knows solution to this problem? Praveen