From chemistry-request@server.ccl.net Mon Sep 13 06:26:35 1999 Received: from mail-b.bcc.ac.uk (mail-b.bcc.ac.uk [144.82.100.22]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA12163 for ; Mon, 13 Sep 1999 06:26:35 -0400 Received: from biochem.ucl.ac.uk (actually host bsmori1.biochem.ucl.ac.uk) by mail-b.bcc.ac.uk with SMTP (XT-PP) with ESMTP; Mon, 13 Sep 1999 11:18:39 +0100 Received: from bsmir18.biochem.ucl.ac.uk (bsmir18 [128.40.46.21]) by biochem.ucl.ac.uk (8.9.2/8.9.1) with ESMTP id LAA23329 for ; Mon, 13 Sep 1999 11:18:39 +0100 (BST) Received: from localhost (nobeli@localhost) by bsmir18.biochem.ucl.ac.uk (8.9.3/8.9.3) with SMTP id LAA10743 for ; Mon, 13 Sep 1999 11:18:39 +0100 (BST) X-Authentication-Warning: bsmir18.biochem.ucl.ac.uk: nobeli owned process doing -bs Date: Mon, 13 Sep 1999 11:18:39 +0100 (BST) From: Irene Nobeli X-Sender: nobeli@bsmir18 To: Computational Chemistry List Subject: Chemical diversity and metabolome Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all I have two questions: a) Does anyone know or have heard of the existence of a map of small molecules in the cell? b) This is a bit trickier. I'm looking at ways that one can classify small molecules (by small I mean molecules that are found as ligands). In other words, chemical diversity or molecular similarity, depending on which way you are looking at it. I would be interested in ANY method of classification, no matter whether it is based on structural, or chemical, electrostatic, hydrophilic or hydrophobic or any other property of the system. I know there are quite a few methods out there. I am particularly interested in automated methods (especially freely available ones) but any contribution will be more than welcome. I would appreciate ANY lead that could help me find more information on either of the two subjects. I shall summarise the response. Maany thanks in advance. Irilenia ------------------------------------------------ Irene (Irilenia) Nobeli Biomolecular Structure and Modelling Unit Department of Biochemistry and Molecular Biology University College London Darwin Building Gower Street London WC1E 6BT nobeli@biochem.ucl.ac.uk 0171-419 3890 0171 504 2171 >>> Pain and suffering are inevitable but misery is optional. <<< From chemistry-request@server.ccl.net Mon Sep 13 10:03:16 1999 Received: from gerwazy.chem.uni.wroc.pl (gerwazy.chem.uni.wroc.pl [156.17.103.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA14158 for ; Mon, 13 Sep 1999 10:03:14 -0400 Received: from wchuwr.chem.uni.wroc.pl ([156.17.103.1]) by gerwazy.chem.uni.wroc.pl (8.8.8+Sun/8.8.8) with ESMTP id PAA24790 for ; Mon, 13 Sep 1999 15:21:26 +0200 (MET DST) Received: from WCHUWR/SpoolDir by wchuwr.chem.uni.wroc.pl (Mercury 1.43); 13 Sep 99 15:16:46 MET Received: from SpoolDir by WCHUWR (Mercury 1.43); 13 Sep 99 15:15:19 MET From: "Andrzej Szymoszek" Organization: University of Wroclaw (Chemistry) To: chemistry@ccl.net Date: Mon, 13 Sep 1999 15:15:11 MET Subject: CCL: Summary: ab initio MD code Priority: normal X-mailer: Pegasus Mail v3.40 Message-ID: Some time ago, I posted the question about the ab initio MD codes available for research. I received answers, for which I am thankful. Here's the summary. The first part is based on what Kari Laasonen (kel@troy.oulu.fi) has written: I found few freeware CP code and there are several inexpensive (?) well tested versions of CP program (or ab initio MD) for more serious modelling. The free ones (I haven't try it) http://poirot.sissa.it/~cava/CP/carpar_pub.html JEEP (by F. Gygi) http://irrmawww.epfl.ch/fg/jeep/jeep.html (see also http://www.llnl.gov/str/Gygi.html) The not free ones: ------ 1 ----- One is the Vienna code by J. Hafners group (mainly G. Kresse) http://tph.tuwien.ac.at/~vasp/ VAMP/VASP is not public domain - if you are interested in this package please contact our boss Prof. Hafner at jhafner@tph.tuwien.ac.at. ----- 2 ------- Another is the FHI code: http://www.FHI-Berlin.MPG.DE/th/fhimd/ If you are interested in testing the FHI98md program package, you can download a demo version. The limited demo version (binary only) is available for free for various platforms. It has a built-in upper limit of eight atoms per cell but no other restriction. If you like to use the full FHI98md program package (source code), you have to register via our registration page. But please note: The FHI98md program package is available for a cover charge of US$ 300 (on request we may grant exceptions, e.g., for colleagues from developping countries). means to accept our license terms . ------- 3 ------- The Parrinello's code is not freely aviable. I dont know the terms to get the code. See http://parrserv2.mpi-stuttgart.mpg.de/ There are many more groups having a good CP code P.S. Our own CP code (FINGER) is not well documented and not very usefull for non-experts. That would be Kari's contribution. Next, Andrew Horsfield, andrew.horsfield@materials.ox.ac.uk, who can help but it is to be mentioned that in the code he means there has not yet been solved the problem of mixed quantum-classical interactions. And last but not least: I received a couple of letters from MSI people. They offer CASTEP and DMOL. The MSI person to be contacted depends on the country where the inquirer lives- see www.msi.com. It is interesting that researchers from Poland- maybe other countries as well- have a "country-wide" license for using the MSI software. Thanks to all for providing useful information, Andrzej Szymoszek From chemistry-request@server.ccl.net Mon Sep 13 12:24:00 1999 Received: from dalton.quimica.unlp.edu.ar (root@dalton.quimica.unlp.edu.ar [163.10.18.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA14789 for ; Mon, 13 Sep 1999 12:23:41 -0400 Received: from jubert2.quimica.unlp.edu.ar (jubert2.quimica.unlp.edu.ar [163.10.18.2]) by dalton.quimica.unlp.edu.ar (8.9.0/8.9.0) with SMTP id NAA18129 for ; Mon, 13 Sep 1999 13:03:11 -0300 Message-Id: <3.0.1.32.19990913131606.0069d51c@dalton.quimica.unlp.edu.ar> X-Sender: pis_diez@dalton.quimica.unlp.edu.ar X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Mon, 13 Sep 1999 13:16:06 -0300 To: chemistry@ccl.net From: Reinaldo Pis Diez Subject: Ab initio MD codes again Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear netters, Does anybody know if any of the AI-MD codes mentioned by Andrzej Szymoszek allow the treatment of spin-polarized systems? The fhi98md code doesn't do it as far as I know. I wonder if VASP and the Parrinello's code do. Thanks in advance. Regards, Reinaldo From chemistry-request@server.ccl.net Mon Sep 13 08:56:59 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 IAA13856 for ; Mon, 13 Sep 1999 08:56:59 -0400 Received: from harfang.CC.UMontreal.CA (harfang.CC.UMontreal.CA [132.204.2.102]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id IAA01352 for ; Mon, 13 Sep 1999 08:51:33 -0400 (EDT) Received: from balzac.CERCA.UMontreal.CA (balzac.CERCA.UMontreal.CA [132.204.150.21]) by harfang.CC.UMontreal.CA (8.8.8/8.8.8) with ESMTP id IAA09882 for ; Mon, 13 Sep 1999 08:51:19 -0400 (EDT) Received: from pellan.CERCA.UMontreal.CA (pellan.CERCA.UMontreal.CA [132.204.150.49]) by balzac.CERCA.UMontreal.CA (8.9.3/8.9.3) with ESMTP id KAA27139 for ; Sat, 11 Sep 1999 10:34:48 -0400 (EDT) From: Suzanne Sirois Received: (from siroiss@localhost) by pellan.CERCA.UMontreal.CA (980427.SGI.8.8.8/8.8.8) id KAA43856 for chemistry@www.ccl.net; Sat, 11 Sep 1999 10:34:48 -0400 (EDT) Message-Id: <199909111434.KAA43856@pellan.CERCA.UMontreal.CA> Subject: 1) Ab Initio 2) HIV Protease To: chemistry@www.ccl.net Date: Sat, 11 Sep 1999 10:34:47 -0400 (EDT) X-Mailer: ELM [version 2.4ME+ PL53 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CClers First Question; ab initio calculations I have lot of experience with DFT and little with HF/Post-HF. I would like to perform some ab initio calculations. I have a system of about 20 atoms containing very important H-bonds. What will be the State-of the Art to optimizing minima and TS followed with an IRC. Someone suggested to me to do the following: Perform a full optimization at RHF/6-31G** of the 2minima and TS. Connect the TS to the two minima with IRC using the GS2 method at the RHF/6-31G**. Then perform an MP2 single point calculation on the 2 minima and TS for obtaining a better energy. Is this the best possible approach? Second Question: I am a little confuse with the following: In JACS 118, 3946 (1996) Citing the author: " It follows from this structure (ref. Wlodawer et al. Science 1989, 245, 616-621) that the two side chains of Asp25-and Asp-25' of the active site are planar with a structural water bound to both." I have downloaded the PDB file: 3HVP and there is no water molecules attach to it. My question is: is there a water molecule in the active site of the wild type enzyme or there is no water molecule. Kind Regards to all of you. Suzanne Sirois From chemistry-request@server.ccl.net Mon Sep 13 09:46:31 1999 Received: from harfang.CC.UMontreal.CA (harfang.CC.UMontreal.CA [132.204.2.102]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA14063 for ; Mon, 13 Sep 1999 09:46:31 -0400 Received: from balzac.CERCA.UMontreal.CA (balzac.CERCA.UMontreal.CA [132.204.150.21]) by harfang.CC.UMontreal.CA (8.8.8/8.8.8) with ESMTP id JAA25637 for ; Mon, 13 Sep 1999 09:41:07 -0400 (EDT) Received: from pellan.CERCA.UMontreal.CA (pellan.CERCA.UMontreal.CA [132.204.150.49]) by balzac.CERCA.UMontreal.CA (8.9.3/8.9.3) with ESMTP id JAA10548; Mon, 13 Sep 1999 09:41:15 -0400 (EDT) From: Suzanne Sirois Received: (from siroiss@localhost) by pellan.CERCA.UMontreal.CA (980427.SGI.8.8.8/8.8.8) id JAA46574; Mon, 13 Sep 1999 09:41:14 -0400 (EDT) Message-Id: <199909131341.JAA46574@pellan.CERCA.UMontreal.CA> Subject: 1)Ab initio 2) HIV-PR To: chemistry@ccl.net Date: Mon, 13 Sep 1999 09:41:14 -0400 (EDT) Cc: siroiss@CERCA.UMontreal.CA (Suzanne Sirois) X-Mailer: ELM [version 2.4ME+ PL53 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CClers First Question; ab initio calculations I have been using DFT for various types of H-bonded systems and to my knowledge it is fast and reliable. I would like to perform some ab initio calculations. I have a system of about 20 atoms containing very important H-bonds. What will be the State-of the Art for optimizing the minima and TS and then examining the IRC. Someone suggested to me to do the following: Perform a full optimization at RHF/6-31G** of the 2minima and TS. Connect the TS to the two minima with IRC using the GS2 method at the RHF/6-31G**. Then perform an MP2 single point calculation on the 2 minima and TS for obtaining a better energy. Second Question: I am a little confuse with the following: In JACS 118, 3946 (1996) Citing the author: " It follows from this structure (ref. Wlodawer et al. Science 1989, 245, 616-621) that the two side chains of Asp25-and Asp-25' of the active site are planar with a structural water bound to both." I have downloaded the PDB file: 3HVP and there is no water molecules attach to it. Is there a water molecule in the active site of the wild type enzyme or there is no water molecule. In fig.4 Science 245, 616 (1989). The authors mention: "Active site electron density showing a density for a water molecule which is found in similar position in all native structures of aspartic proteases." (Could it be a density for something else (NH4+?). "The distance of this water from the carboxylate O atoms is slightky greater than expected". (Why modeling the HIV-Pr with a water molecule in the catalytic site cleft if the crystal structure reveals that the water is at a distance greater than expected?) Kind Regards to all of you. Suzanne Sirois From chemistry-request@server.ccl.net Mon Sep 13 15:06:33 1999 Received: from earth.ox.ac.uk (darwin.earth.ox.ac.uk [163.1.22.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA15666 for ; Mon, 13 Sep 1999 15:06:33 -0400 Received: from wowbagger.earth.ox.ac.uk (wowbagger [163.1.22.29]) by earth.ox.ac.uk (8.9.3+Sun/8.9.1) with ESMTP id UAA21718; Mon, 13 Sep 1999 20:00:59 +0100 (BST) From: Keith Refson MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <14301.18921.401079.283684@gargle.gargle.HOWL> Date: Mon, 13 Sep 1999 20:00:57 +0100 (BST) To: Reinaldo Pis Diez Cc: chemistry@ccl.net Subject: CCL:Ab initio MD codes again In-Reply-To: <3.0.1.32.19990913131606.0069d51c@dalton.quimica.unlp.edu.ar> References: <3.0.1.32.19990913131606.0069d51c@dalton.quimica.unlp.edu.ar> X-Mailer: VM 6.75 under 20.4 "Emerald" XEmacs Lucid Reinaldo Pis Diez writes: > Does anybody know if any of the AI-MD codes mentioned by Andrzej > Szymoszek allow the treatment of spin-polarized systems? > The fhi98md code doesn't do it as far as I know. I wonder if VASP and the > Parrinello's code do. Both VASP and CASTEP are able to do spin-polarized calculations. So can one more plane-wave code which was not mentioned, FEMD, written by Ali Alavi now at Queens University, Belfast. I don't know his position on sharing the code however. It is perhaps also worth mentioning that CASTEP is available free of charge in source code form to all UK academics under an agreement between MSI and the UK Car-Parrinello consortium. I can't find the original question to see the exact scope, but you can also perform ab-initio MD with two other non-plane-wave codes I know of, SIESTA which is a local-orbital periodic DFT code from Madrid (P. Ordejon et al Phys. Rev B51 (1995) 1456-1476), and WIEN95 (98?) which is a LAPW code from Karl-Heinz Schwarz's group in Vienna. I can't be sure, but I also have a vague recollection that AMD (Amsterdam Density Functional) also does MD. Keith Refson -- Dr Keith Refson, "Paradigm is a word too often used by those who would Dept of Earth Sciences like to have a new idea but cannot think of one." Parks Road, -- Mervyn King, Deputy Governor, Bank of England Oxford OX1 3PR, UK Keith.Refson@ Tel: 01865 272026 earth.ox.ac.uk Fax: 01865 272072 From chemistry-request@server.ccl.net Mon Sep 13 23:31:04 1999 Received: from mxout1.cac.washington.edu (mxout1.cac.washington.edu [140.142.32.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id XAA18993 for ; Mon, 13 Sep 1999 23:31:04 -0400 Received: from mailhost2.u.washington.edu (mailhost2.u.washington.edu [140.142.33.2]) by mxout1.cac.washington.edu (8.9.3+UW99.09/8.9.3+UW99.08) with ESMTP id UAA28063; Mon, 13 Sep 1999 20:25:09 -0700 Received: from [140.142.174.51] (cs311-50.spmodem.washington.edu [140.142.174.51]) by mailhost2.u.washington.edu (8.9.3+UW99.09/8.9.3+UW99.08) with ESMTP id UAA04524; Mon, 13 Sep 1999 20:25:08 -0700 Message-Id: <199909140325.UAA04524@mailhost2.u.washington.edu> X-Mailer: Microsoft Outlook Express Macintosh Edition - 4.5 (0410) Date: Mon, 13 Sep 1999 20:26:39 -0700 Subject: Viewing MOLCAS Molecular Orbitals From: "Eric C. Brown" To: chemistry@ccl.net Mime-version: 1.0 X-Priority: 3 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Dear CCLers, We are interested in viewing molecular orbitals (graphically) from MOLCAS v.4 calculations. Our current setup allows us to use Chem3D Ultra and read in Gaussian 98 .cub files, which allows us to ensure that the active space is, indeed, the relevant selection. In addition to Gaussian 98 results, we also wish to do the same with MOLCAS calculations. Does anyone know of a way to view these orbitals, or even better, how to convert them to the cubegen file format? Any and all help is appreciated! Eric Brown University of Washington Department of Chemistry P.S. Could you please cc: my email as well as the list?