From h8714031@hkuxa.hku.hk Wed Feb 17 00:26:24 1993 From: h8714031@hkuxa.hku.hk (Mok Kam Wah) Message-Id: <9302170428.AA27028@hkuxb.hku.hk> Subject: About Molden2.1 To: chemistry@ccl.net (Computational Chemistry) Date: Wed, 17 Feb 93 12:28:50 WST Dear Netter, Is there anyone modified MOLDEN2.1 so that it can use with GAMESS American version? Any suggestion? Please mail me! Thanks in Advance!! K.W.Mok Email:h8714031@hkuxa.hku.hk From doelz@urz.unibas.ch Wed Feb 17 09:01:19 1993 Date: Wed, 17 Feb 1993 08:01:19 +0100 From: Reinhard Doelz Message-Id: <450*/S=doelz/OU=urz/O=unibas/PRMD=SWITCH/ADMD=ARCOM/C=CH/@MHS> To: grzesb (Receipt Notification Requested) (Non Receipt Notification Requested) Subject: DMOL electrostatics: reply on DIBUG list I read the description on chemistry@osc edu and forwarded it to the BIOSYM group. Reply follows. regards Reinhard ================== From: To: Subject: dmol electrostatic potentials There is a bug in DMol version 2.2 in the calculation of electrostatic potentials, as reported by Grzegorz Bakalarski. This has been corrected in version 2.3, which is (as of this week) the current version. DMol users may report bugs directly to rcenter@biosym.com. Michael Wrinn ____________________________________________________________________________ The following information is automatically appended by the mailer. This list is called DIBUG@COMP.BIOZ.UNIBAS.CH and covers the Discover, Insight and Biosym products User group. Mail (un)subscribe messages to DIBUG-REQUEST@COMP.BIOZ.UNIBAS.CH, other to DIBUG-ADMIN@COMP.BIOZ.UNIBAS.CH The archive is available on bioftp.unibas.ch as FTP and GOPHER service. ========= From UDIM018@FRORS31.bitnet Wed Feb 17 05:24:07 1993 Message-Id: <199302170844.AA04350@oscsunb.ccl.net> Date: 17 Feb 93 09:24:07 EDT From: Subject: Zeolite and Alumina data bases To: chemistry@ccl.net E. M. EVLETH Dynamique des Interactions Moleculaires Universite Pierre et Marie Curie 4 Place Jussieu, Tour 22, Paris 75005 33-1-44-27-42-08 (work), 33 = France; 1 = Paris 33-1-45-48-67-20 (home) FAX 33-1-44-27-42-17 e-mail UDIM018 at FRORS31.bitnet Information; I am looking for ftp transferable or discette databases on zeolite structures (mainly), Alumina, and inorganic crystal structures. In "Modeling of Structure and Reactivity in Zeolites" (AP 1992), edited by C.R.A. Catlow, Freeman et al article on Zeolite Computer Graphics sites a reference (4) of a "Zeofile", by J. M. Newsam and M. M. J. Treacy, but unpublished and in preparation for submittal to the journal Zeolites. This review published last year an Apdate on the Atlas to Zeolite Structure Types. However, journal published data is sometimes incomplete and typo errors will appear on transfer. Obviously I want to avoid plowing through the Cambridge Data Base and looking for a truncated version in a specific area of interest. I am not looking for a freebie so any commerical proposal is welcome. E. M. Evleth, From h8714031@hkuxa.hku.hk Wed Feb 17 11:27:00 1993 Date: Wed, 17 Feb 93 23:33:42 WST From: h8714031%hkuxa.hku.hk@OHSTVMA.ACS.OHIO-STATE.EDU Subject: Summary Results of MO plotting program! To: chemistry@ccl.net Message-Id: <9302171533.AA14822@hkux2.hku.hk> Dear Netters, Thanks a lot for all suggestion and advice! Here is the summary of the suggestion I received. This is the ony way I can contribute to the net news. Hope that this is useful to you. In Short, there are three packages available: MOLDEN, PSI88 and xpsi. Dr Jan Hrusak writes, ===================================================================== There is a program PSI88 (or mayby a later version) for a 3D Orbital plot. It has also an interface to GAUSSIAN-XX series programs, and the eigenvector can be extracted from the checkpoint file. Authors: William L. Jorgensen Daniel L. Severance Department of Chemistry Yale University P.O. Box 6666 New Haven, CT 06511, USA. Phone (203) 432-6288 Fax (203) 432-6144 Internet: dan@rani.chem.yale.edu Dan Severance informed me, he is still working on the source and so try to get more informations from the attached E-Mail ====================================================================== Dr Hans Borkent writes, ====================================================================== Regarding your request for a plotting program: My colleague Gijs Schaftenaar is developing a program for this purpose named MOLDEN. It runs on several platforms (a.o. X) and reads output >from Gamess and Gaussian, and after modifying the ouput, from AMPAC/ MOPAC as well. Postscript output is included, etc. It is available from QCPE (no. 619). Those you interested in latest version, please Contact Gijs Schaftenaar schaft@caos.kun.nl, tel +31-80-652248 We hope it is of any help and appreciate remarks on the use of MOLDEN. ========================================================================== Dr Eberhard writes, ========================================================================= There is a PD program called PSI88. It is written in fortran and has interfaces to Gaussian and Mopac. I think that it isn't too difficult to write the gamess. (I must confess that I have the plan to write it but havn't got time to do it). I have modified the graphic-routines so that one can select X11,hpgl,ps(Monochr.),Laserjet/Deskjet(Monochrome). =========================================================================== Dr pedro writes, =========================================================================== If you have acces a unix machine running X11 release 5 or to a PEX-5.0/PEX-5.1 Xterm try our xpsi. It plots 3D volumes on screen, you can rotate to see better and it produces an output suitable for rayshade4.0 render a high quality picture. regards pedro PS: xpsi is on pub/chemistry at iqm.unicamp.br (143.106.1.37) ============================================================================= Thanks again K.W.Mok h8714031@hkuxa.hku.hk From wipke@SECS.UCSC.EDU Wed Feb 17 01:45:07 1993 Date: Wed, 17 Feb 1993 09:45:07 PST From: "W. Todd Wipke" To: chemistry@ccl.net Message-Id: <00968430.AB64B940.32413@SECS.UCSC.EDU> Subject: Final Call Summer Undergraduate Research Fellowship (SURF) This is a 10 week $2500 stipend program to do research with faculty at UCSC in Chemistry/Biochemistry. You must be a citizen of the USA, in your Junior year now. There are a wide variety of research projects available, including particularly computational chemistry, with a special symposium devoted to the latter topic for SURF students. The Institute for Scientific Information listed UC Santa Cruz as the Number One in the USA in terms of frequency of citation in the literature on a per paper basis for the Natural Sciences, number 14 in biological sciences. For further information, call (408) 459-4002 or send email to "troche@chemistry.ucsc.edu" From DSMITH@uoft02.utoledo.edu Wed Feb 17 09:15:16 1993 Date: Wed, 17 Feb 1993 14:15:16 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: Re: Summary Results of MO plotting program! To: h8714031%hkuxa.hku.hk@OHSTVMA.ACS.OHIO-STATE.EDU Message-Id: <01GUTX9W1QCO0002NX@UOFT02.UTOLEDO.EDU> I suppose that I have talked so much about the AVS Chemistry Viewer on this mail exploder that I just did not bother this time. Molecular Simulations, Inc. has a package for visualization, graphical input and analysis of results from Gaussian 9x and MOPAC 5/6. I understand that a GAMESS module may soon be available. Orbital plotting, density plotting, and various representations of the molecular structure are only a few of the features available in this package. Doug Douglas A. Smith Assistant Professor of Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu ========================= Dear Netters, Thanks a lot for all suggestion and advice! Here is the summary of the suggestion I received. This is the ony way I can contribute to the net news. Hope that this is useful to you. In Short, there are three packages available: MOLDEN, PSI88 and xpsi. K.W.Mok h8714031@hkuxa.hku.hk From jpoole@oucsace.cs.ohiou.edu Wed Feb 17 11:39:04 1993 Date: Wed, 17 Feb 93 16:39:04 EST From: James Poole Message-Id: <9302172139.AA23823@oucsace.cs.ohiou.edu> To: CHEMISTRY@ccl.net Subject: Using Partial Coordinates in CHARMM Hello Fellow Computational Chemistry Mailing List Readers, I have a small problem setting up a protein structure in CHARMM that someone here may know the answer. I am working on a model of a coiled-coil protein. I have the alpha helices defined as I need them but I am having difficulty getting the left-handed super-coiling of the two alpha helices. The last approach that I have used seems to be the most reasonable method for getting the backbone dihedrals defined to give the required coiled-coil. This approach is to use the C-alpha coordinates for tropomyosin from the Brookhaven PDB as a template. What I attempted was to read in the sequence of my protein into CHARMM and set up the internal coordinates >from the parameter files like normal. The next step was to read in the coordinates of the Tm C-alphas from a file modified to have the correct residue names and numbers and then build the coordinates, energy minimize with constraints, and dock the two helices. The snag is that the read-in coordinates are overwritten when the remaining coordinates are build (unexpected based on the manuals). What I am interested in knowing is has anyone used partial defined coordinates and then built the remaining ones succesfully and if so will you share your wisdom. I have also sent this to the CHARMM mail-exploder and have a call into MSI, but this seems to be the best resource for practical experience. Thanks in advance, Jim Poole, (614) 593-1744 voice Ohio University, (614) 593-llll fax Dept. of Chemistry jim@quanta.phy.ohiou.edu or jpoole@oucsace.cs.ohiou.edu ---- begin sample charmm code ---- > > start of charmm code omitted > > GENE HLXA SETU > > IC PARA > OPEN READ CARD UNIT 14 NAME INPUT.CRD > READ COOR CARD UNIT 14 > CLOSE UNIT 14 > IC BUILD > > remainder of code omitted > From hcj@gull.uncc.edu Wed Feb 17 12:13:21 1993 Date: Wed, 17 Feb 93 17:13:21 -0500 From: hcj@gull.uncc.edu (Harry C. Johnson) Message-Id: <9302172213.AA14079@gull.uncc.edu> To: CHEMISTRY@ccl.net Subject: MM2 energy minimization? In testing our geometry optimization program that utilizes genetic algorithms, we were able to obtain a lower energy conformation than MM2. This is not too suprising, however, when we gave our new geometry to MM2, it calculated an initial energy of ~9.44 and ended with a final energy, after _minimization_, of ~10.05!! I was just curious why this might be? Any ideas? ============================================================================= Harry C. Johnson IV Phone: (704)547-4339 E-Mail: hcj@gull.uncc.edu Department of Chemistry University of North Carolina at Charlotte Charlotte, North Carolina 28223 "Seems to me, its all just chemistry..." -Neil Peart =============================================================================