From CTARG@Levels.UniSA.Edu.Au Tue Sep 28 22:16:17 1993 Date: Tue, 28 Sep 1993 12:46:17 +0930 From: CTARG@Levels.UniSA.Edu.Au Subject: parameters for molecular modeling To: chemistry@ccl.net Message-Id: <01H3HDGA4H4Y9AMH6T@Levels.UniSA.Edu.Au> Dear Netters, I've recently started on some molecular modelling work only to find that the parameters for the elements I want to use are not available. I realise torsion angles and bond lengths are easily available from crystallographic data but what about Gasteiger charge coefficients and Vand der Waals parameters for nonbonded interactions? Are there any programs available which will iteratively calculate these things from a supplied structure? Any advice/references will be greatly appreciated. Thanks Andy. From AZHARI%EGFRCUVX.BITNET@phem3.acs.ohio-state.edu Tue Sep 28 14:43:25 1993 Date: Tue, 28 Sep 1993 14:43:25 +0000 (O) From: AZHARI%EGFRCUVX.BITNET@phem3.acs.ohio-state.edu Subject: GAMESS-UK To: chemistry@ccl.net Message-Id: <01H3HHJJSKLU000GI2@EGFRCUVX.BITNET> Hi netters: Dose anyone know who to obtain the GAMESS-UK program (a public domain would be much better) and if it dose MP2 force field calculation and approximate cost. Thnaks. Adel El-Azhary From phil@ovid.med.utoronto.ca Tue Sep 28 05:34:53 1993 From: phil@ovid.med.utoronto.ca (Philip Tole) Message-Id: <9309281334.AA01259@ovid.med.utoronto.ca> Subject: Is there parallel code for MD? To: CHEMISTRY@ccl.net Date: Tue, 28 Sep 1993 09:34:53 -0400 Dear netters, does anybody know if there is parallel code available for molecular dynamics methods ? Thanks in advance Philip Tole From JAMES@UNCA.EDU Tue Sep 28 06:42:05 1993 Date: Tue, 28 Sep 1993 10:42:05 -0400 (EDT) From: "Charles G. James" Subject: Re: List of Molecular Modeling Programs To: vdvk@netcom.com Message-Id: <01H3H81M6YBM8WWVU0@UNCA.EDU> Organization: University of North Carolina at Asheville vdvk@netcom.com writes: >I would like to propose to create a list, as complete as possible, of >molecular modeling programs. >The programs MUST be able to display a molecular structure from Cartesian, >internal, or fractional coordinates. I have a question. This is probably only because I have some definitions confused but, how do you define the difference between a program which only displays a molecule graphically from some sort of input file, such as Ball and Stick or XMOL, and a program which takes the input structure and does some type of computations with the data such as MOPAC or MM3. These calculations can be some type of geometry optimization or vibrational prediction, but in any case calculations are performed in which the input structure may be changed. I have now heard both types of programs called "molecular modeling programs". There are programs we use here, old ones granted, which are called "molecular modeling programs" that do not have the graphical presentation built into the calculation program. Still we call them molecular modelers because they use some sort of mathematical model to represent the behavior or structure of the molecule. Should we not call them that because they cannot display molecular structures? Charles G James Chemistry Department University of North Carolina at Asheville. One University Heights Asheville, NC 28804-3299 Phone: 704-251-6443 james@unca.edu From chris@glycob.ox.ac.uk Tue Sep 28 12:04:43 1993 Date: Tue, 28 Sep 1993 16:04:43 EDT From: chris@glycob.ox.ac.uk To: chemistry@ccl.net Message-Id: <009733A1.A55E9720.9539@glycob.ox.ac.uk> Subject: Simulated annealing in solvent Hello netters Our group is interested in performing simulated annealing on a carbohydrate solute in water solvent. Using the Berendsen coupling algorithm within Amber, we have carried this out using a single coupling constant of 0.25 ps and heating the system to 1000 K followed by slow cooling to 300 K. The result appears to be "hot solvent/cold solute". Can anyone give us any indication of how to avoid this e.g. by using separate temperature coupling constants? If so, does anyone have suitable values for the temperature coupling constants? Any references would be most useful. Thank you all in advance for your time. *************************************************************** * Dr. Chris. Edge * Tel. +44-865-275-338 * * Glycobiology Institute * Fax. +44-865-275-216 * * Oxford University * e-mail chris@glycob.ox.ac.uk * * South Parks Road * 100117.3646@compuserve.com * * Oxford OX1 3QU U.K. * * *************************************************************** From feng@lisboa.ks.uiuc.edu Tue Sep 28 06:30:01 1993 From: Zhou Feng Message-Id: <9309281630.AA00329@lisboa.ks.uiuc.edu> Date: Tue, 28 Sep 93 11:30:01 -0500 To: chemistry@ccl.net Subject: looking for modelling position in pharmaceutical company Dear netters: I am interested in doing a survey of molecular modelling positions in pharmaceutical companies, especially middle size (or large companies). Does anybody know what is an effective way for me to 1. find a background description for these companies, how are they doing in the recent years 2. find out whether they have positions for molecular modelling and what kind of modelers do they want ? Appreciated if you send your reply to the net, or to my email address. Feng From X0ZHAO01@ULKYVX.LOUISVILLE.EDU Tue Sep 28 07:46:43 1993 Date: Tue, 28 Sep 1993 12:46:43 -0500 (EST) From: LIU JIANLING Subject: CSD, FDAT --> MAC MIMIC or CHEM 3D To: chemistry@ccl.net Message-Id: <01H3HD8WSCWY935OKR@ULKYVX.LOUISVILLE.EDU> dear netters: please tell me how I can use the file in FDAT format (got from CSD ) as input file to MAC MIMIC or CHEM3D.It seems to me that I need to change some "heading" of the FDAT file in some way (use a text editor) in order to adjust the NEW environment in MAC MIMIC or CHEM3D....but I don't know the "skill" ! help,help! cheers From gl@beta.mdy.univie.ac.at Tue Sep 28 18:08:35 1993 Message-Id: <199309281742.AA26407@oscsunb.ccl.net> From: Gerald Loeffler To: CHEMISTRY@ccl.net Subject: force fields for biomolecules Date: Tue, 28 Sep 93 17:58:30 MEZ Dear Chemist! We have been using the GROMOS force field implemented in the program gromos itself and in a home-made program for the MD-simulation of proteins in water for a long time. Since I consider this force field somewhat dated by now, I am asking you for your experience with FORCE FIELDS FOR BIOMOLECULES. I would very much appreciate answers to the following questions: 1) what is the force field you would recommend and which program you are using implements this force field 2) why would you recommend this force field - e.g. are there published comparisons between different force fields? 3) is source code for a program using this force field available? What I ideally would like to get is a reference to a paper describing the force field in detail and a 'sample implementation' by the developers of the force field including source code. Using that I will probably write a program that uses this force field on my own, since we are usually doing a lot of algorithmic tuning. I THANK YOU VERY MUCH FOR YOUR RESPONSES IN ADVANCE, Gerald -- +------------------------+ +-----------------------------------+ |Gerald Loeffler | |Theoretical Biochemistry Group | |gl@beta.mdy.univie.ac.at| |Department of Theoretical Chemistry| +------------------------+ |University of Vienna | +-----------------------------------+ +--------------------------------------------------------------------------+ |Institut fuer Theoretische Chemie und Strahlenchemie der Universitaet Wien| |Arbeitsschwerpunkt Theoretische Biochemie | |Waehringerstrasse 17/Erdgeschoss | |A-1090 Wien, Austria | +--------------------------------------------------------------------------+ From kb7@tower.york.ac.uk Tue Sep 28 20:32:12 1993 Date: Tue, 28 Sep 1993 19:32:12 +0100 (BST) From: K Bryson Subject: Dihedral energy barriers. To: chemistry@ccl.net Message-Id: Hi, I'm wondering if anyone can provide good references for tables containing energy levels against torsional changes in small organic molecules ( Amines in particular ). Even better would be a computer database site for commonly used force field parameters for small organics. Is it general policy to update torsion parameters after calculating partial charges for a new molecule or are accepted torsional parameters for the atom types ( say in Amber or CharmM ) used more often ? Do people use QM packages to calculate torsion parameters or do they try to use experimental when available ? Thanks, Kev. ----------~~~~~~------~~~~~~~~~~---------------~~~~~----------~~~~~-- K.Bryson email: kb7@tower.york.ac.uk Biophysics Group Tel : +44 904 430000 Extn. 2236 Physics Department Fax : +44 904 432214 University of York Heslington "Molecular modelling of DNA and its YORK, UK interaction with small molecules." YO1 5DD -------------------~~~~~-------------~~~~--------~~~~--------~~~~~--- From DSMITH@uoft02.utoledo.edu Tue Sep 28 10:04:49 1993 Date: Tue, 28 Sep 1993 15:04:49 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: reviewers and computational resources To: chemistry@ccl.net Message-Id: <01H3HHPTL98I003R8N@UOFT02.UTOLEDO.EDU> These comments are made without reference to any particular individual or institution. Please do not take offense. In recent weeks I have received, either in my capacity as an author or as an editor, comments on manuscripts and proposals which bother me somewhat. In particular, referees have made statements suggesting that current hardware and software are such that the level of theory in a particular study needs to be increased, i.e. the reviewer believes that the problem was/will be attacked at too low a level of theory. "Certainly," these reviewers state, "the current technology would allow this work to be done at a significantly higher level of theory than the author reports." In some cases I agree with this sentiment. Certain problems require a minimum level of theory. In other cases this is just not necessary. Sure, we can do some molecules and systems using extremely large basis sets and lots of correlation. Or at least our hardware and software are capable of doing that. But do we always have those resources available? If we are using a Supercomputer Center, our resource unit allowance is limited. To run some of these monster calculations would require half a Cray-year in some cases, given the size of the system, the number of calculations to be run, etc. If we use in-house computers, do we really have that much control over shared resources, and will other researchers give up all their access in order to satisfy these reviewers? I consider my research group to be resource rich, given the number, size and type of workstations and the amount of Cray time we have available. And I sometimes may fall prey to this same snobbery, that the calculations should have been done bigger and better. But not everyone (including me, sometimes) is able to do bigger and better. And in many situations (e.g. industrial problems) bigger is NOT better, because it is more expensive, takes more time, and does not substantially improve the answers (i.e. the trends are the same at lower levels of theory, so the direction provided by the calculation doesn't change at higher levels). As scientists, we should always strive to do the best possible job, given the resources available. We should also choose our research problems such that we can do the research right, and (hopefully) get the right answers to our questions, within our resources. But are we correct in saying to others "Do the calculations at MP3/6-311G** rather than MP2/6-31G*, because your computers and software are able to handle it"? Comments and discussion are welcome. Please confine flames to personal responses rather than the net. Doug Douglas A. Smith Assistant Professor of Chemistry and of Medicinal and Biological Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu From d3f012@pellucidar.pnl.gov Tue Sep 28 07:45:02 1993 Date: Tue, 28 Sep 93 14:45:02 -0700 From: d3f012@pellucidar.pnl.gov Subject: cyclodextrins To: chemistry@ccl.net Message-Id: <9309282145.AA23130@pellucidar.pnl.gov> I'd like to hear from anyone who has experience (or knows of someone) with molecular mechanics MD simulations of cyclodextrins. Are there any of the standard force fields that have parameters for carbohydrates that have been shown to do an adequate job on these types of systems? Mark Thompson ************************************************************************** Mark A. Thompson Sr. Research Scientist email: d3f012@pnlg.pnl.gov Molecular Science Research Center FAX : 509-375-6631 Pacific Northwest Laboratory voice: 509-375-6734 PO Box 999, Mail Stop K1-90 Richland, WA. 99352 Argus available via anonymous ftp from pnlg.pnl.gov (130.20.64.11) (in the argus directory). Download the README file first. Disclaimer: The views expressed in this message are solely my own and do not represent Battelle Memorial Institute, Pacific Northwest Laboratory, or any of its clients. ************************************************************************** From hogue@calumet.den.mmc.com Tue Sep 28 10:54:41 1993 Date: Tue, 28 Sep 93 16:54:41 MDT From: hogue@calumet.den.mmc.com (Pat Hogue 1-2183) Message-Id: <9309282254.AA03448@calumet.den.mmc.com> To: chemistry@ccl.net Subject: Fluorine anion abstraction Dear netters: Fluorine has been observed to leave perfluoropolyethers (especially the -O-CF2-O- group) as the anion. A Lewis acid (electron pair acceptor) can act as the receptor, but a metal with a high coordination number is also capable of abstracting the anion, through what has been described as a nucleophilic mechanism. My question is: why doesn't fluorine leave as an atomic species, e.g., -CX2-CX2- + 2Zn = alkyne + 2ZnX2 Pat Hogue From gg339@jarvis.pnl.gov Tue Sep 28 10:04:55 1993 Date: Tue, 28 Sep 93 17:04:55 -0700 From: gg339@jarvis.pnl.gov Subject: heme electronic structure calcs To: chemistry@ccl.net Message-Id: <9309290004.AA19274@jarvis.pnl.gov> Hello Netters, I'm looking for references to electronic structure calculations (at various levels) on heme groups. Any info is greatly appreciated. If response is healthy I'll summarize to the net. Thanks John Manchester Roswell Park Cancer Inst / Battelle PNL voice 509/372-4660 fax 509/375-6631 From h8714031@hkuxa.hku.hk Wed Sep 29 03:08:24 1993 From: h8714031@hkuxa.hku.hk (Mok Kam Wah) Message-Id: <9309290305.AA09939@hkuxb.hku.hk> Subject: Use IRC to cal. a diatomic potential in GAMESS? To: chemistry@ccl.net (Computational Chemistry) Date: Wed, 29 Sep 93 11:05:01 WST Dear Netters, Somebody has suggested me that it may be possible to determind the intermolecular potential of a diatomic use IRC method in GAMESS (USA version). To my understanding, IRC is use to calculate the path which connect the reactants and products through the transition state. Is this possible for me to calculate a bound potential of a diatomic potential? Is there any other method to calculate the potentail in GAMESS? K.W.Mok -- K.W.Mok E-Mail: h8714031@hkuxa.hku.hk Dept. of Chem., University of Hong Kong.