From milan@helix.nih.gov Thu Sep 17 21:21:22 1992 Date: Fri, 18 Sep 92 01:21:22 -0400 From: milan@helix.nih.gov (Milan Hodoscek) To: CHEMISTRY@ccl.net Subject: Tell me which is right, G90 or MOPAC? Hi, Comparing results from different programs I encountered this problem: C6H6 (kcal/mole) MNDO AM1 MOPAC 21.87985 23.06206 G90 21.76903 22.96633 With the following input coordinates: 1scf xyz mndo test for derivatives G90 run is: # mndo force nosymm C 0.0000 0 0.0000 0 0.0000 0 C 0.0000 0 0.0000 0 1.4000 0 C 1.2124 0 0.0000 0 2.1000 0 C 2.4248 0 0.0000 0 1.4000 0 C 2.4248 0 0.0000 0 0.0000 0 C 1.2124 0 0.0000 0 -0.7000 0 H -0.9353 0 0.0000 0 -0.5400 0 H -0.9353 0 0.0000 0 1.9400 0 H 1.2124 0 0.0000 0 3.1800 0 H 3.3601 0 0.0000 0 1.9400 0 H 3.3601 0 0.0000 0 -0.5400 0 H 1.2124 0 0.0000 0 -1.7800 0 Does anybody knows where this small(?) difference comes from. We have problems with derivatives... Milan Hodoscek From ORG3@caos.caos.kun.nl Fri Sep 18 04:13:02 1992 Date: Fri, 18 Sep 1992 09:20:23 METDST From: CMC department Subject: PostDoc Position offered at ORGANON, The Netherlands To: CHEMISTRY@oscsunb.ccl.net Date: 11-Sep-1992 Posted-date: 11-Sep-1992 Postdoctoral fellowship Computational Chemistry Organon International bv - part of the Pharma Division of Akzo - is engaged in the development, production and marketing of drugs for human ethical use. More than 6,000 people are employed world- wide of whom roughly 1,000 are employed in the R&D organisation. Research is focused on fertility control, immunology, (cardio)vascular diseases, the nervous system and cancer. A postdoctoral position (appointment for a maximum of 3 years) is available at the Department of Computational Medicinal Chemistry (CMC) at Oss, the Netherlands. The department aims to support the rational design of biologically active compounds with a pre- defined pharmacological profile. In this respect, computational chemistry techniques (molecular modelling and graphics, energy calculations, QSAR) and database techniques are employed. The department is involved in the development of 3D databases and 3D search techni(e.g. Chemical & Engineering News, August 10, 1992, p 20). Your job will mainly involve the in-house development of CMC methodology. The work will be focused on de-novo drug design approaches and partly be a continuation of 3D search strategies. We expect you to be capable of carrying out a research project in computational chemistry and to have demonstrated this ability by obtaining a PhD degree in chemistry with emphasis on computer applications. At Organon you will find a scientifically stimulating environment and many possibilities for further personal development. We expect you to communicate results at meetings as well as through scientific publications. Salary will be commensurate with experience with a minimum of NLG 5,028 per month. Further information can be obtained from Dr. J.-R. Mellema, head CMC department, +31-4120-62140. Applicants are asked to send in a statement of interest, resumi (CV) and list of publications within 3 weeks from the date of issue to Organon International B.V. attn. J.J.M. Hoeven, Personnel Affairs, P.O. Box 20, 5340 BH Oss, The Netherlands (or faxed to +31-4120-62539). From harry@wpcs01.phys-chemie.uni-wuerzburg.de Fri Sep 18 15:30:50 1992 Date: Fri, 18 Sep 92 13:30:50 +0200 From: Harald Lanig To: CHEMISTRY@ccl.net Subject: Help: Excited states in MOPAC or AMPAC Dear Netters, I have started doing geometry-optimisation using semi-empirical methods (AM1) and have now the task minimizing excited states of heteroaromatic molecules. Calulating excited states of unsubstituted aromates and heteroaromates workes quite well, because the calulated HOMO, where an electron is removed, is a ring-orbital. Difficulties are rising when substituting a H-atom (of benzene) for example with a SO3- group. Looking at the orbitals in the ground-state shows that the HOMO is located on the O-atoms and NOT in the ring. Now my problem: How can I remove one electron of the pi-system to get a normal pi-pi(*)- exitation ? This is important, because the UV-spectras of the substituted molecules are just the same as the unsubstituted ones. (Exciting the side chain (SO3-) will lead into dissociation). What can I do if the "ring-HOMO" of the molecule is the HOMO-6 or even lower ? In this case, a CI-calulation will fail (I think). I hope, somebody can help me. Please answer via e-mail: harry@phys-chemie.uni-wuerzburg.dbp.de Thanks in advance Harald Lanig. From mls@wucmd.wustl.edu Fri Sep 18 04:42:55 1992 Date: Fri, 18 Sep 92 09:42:55 -0500 From: mls@wucmd.wustl.edu (Mark Smythe) To: chemistry@ccl.net Subject: non-aqueous solvation : summary Dear netters, In response to my query on non-aqueous solvation using Amber Charles Foley writes. Some types of non-aqueous simulations can be done with the AMBER code as is. I have run some periodic boundary simulations of a peptide in methanol. The steps involved are: 1) add the methanol parameters to the database. I used the parameters from Jorgensen: J. Phys. Chem. 94, 1683 (1990) J. Phys. Chem. 90, 1276 (1986). 2) Create a PDB file with your solute surrounded by the appropriate box of solvent molecules. 3) Create a prep file for you solvent molecule. 4) Create a link.input file defining the solute and surrounding solvent molecules. Define each solvent molecule as a separate molecule in link. 5) Create an edit.input file that creates a "dummy" box. This means you use the "BOX" option to add waters, but set the closeness of approach parameters so that no waters will actually be added. You should also use the "XRAY" option to read in the PDB file you created above. 6) Create a parm file for the system. Now edit the resulting topology file. Do the following: A) Search the file for a line starting with either "0.90000000E+02" or " .90000000E+02" (depending on whether your system writes the leading 0). This line contains the dimensions of the box. You will need to know these, and replace them in this file. The values on this line are: angle boxx boxy boxz Change only the box dimensions to reflect the size of the box in your PDB file. B) Search *backwards* in the file, starting with the second line above the line you modified in (A), for the first line that contains three, and only three, values. The values on this line are IPTRES NSPM NSPSOL IPTRES: Set to the number of the last *residue* to be considered part of the solute. NSPM: Do not modify NSPSOL: Set to the number of the first *molecule* to be considered part of the solvent. 7) If you are running with SANDER/MINMD, you're done. If you are running with GIBBS, you should set the variable ITIP in the input to 1, to indicate you are using a non-water solvent. That should get you there. I created my starting PDB file using a beta release of LEAP, the graphical AMBER interface. You might be able to get a copy of this through UCSF. The recipe for creating the box in AMBER was done with great help from David Pearlman of Vertex Pharmaceuticals. He is one of the principle authors of AMBER 3.0A and is inimately familiar with the details of the code. You might consider directing any further queries regarding AMBER to the mailing list maintained at UCSF. To subscribe to the list, just send mail > to amber-request@cgl.ucsf.edu. To send queries, comments, whatever, just > send mail to amber@cgl.ucsf.edu. I have had good responses from people who > read that list. > Good Luck! Charles K. Foley, Ph.D. Cray Research, Inc. Americas & Asia/Pacific Group P.O. Box 12746 Research Triangle Park, NC 27709 o <( ckf@f16.cray.com [\. In response to : ... What types (MeOH, DMSO, etc) of different solvent boxes are available that have been suitably parameterised and tested? Sorry, not an Amber user (yet). But for GROMOS, there should be MeOH, CCl4 (but there's a paper, telling full MD in CCl4 is not much better than SD with appropriate parameters) and DMSO (Rao+Singh: JACS _112_, 3803-3811 (1990); Mierke+Kessler: JACS _113_, 9466-9470 (1991) + one more recently, I think). I seem to recall some rumours about CHCl3, but I might be veeery wrong ... Wolfgang. +======================================+=====================================+ | Wolfgang Sauer | | | Institut fuer Organische Chemie I | "You have to be three standard | | Henkestr. 42, D-8520 Erlangen, FRG | deviations away from a normal | | | personality to like UNIX." | | sauer@organik.uni-erlangen.de | | | Tel.: 49/0 - 9131 - 85 - 2952 | Morris Jones (C&T) | | Fax: - 9132 | | +======================================+=====================================+ Thankyou to those who responded Mark ----------------------------------------------------------------------------- | Mark Smythe | Phone : (314) 935 4683 | | Center for Molecular Design | Fax : (314) 935 4979 | | Washington University | E-Mail: mls@wucmd.wustl.edu | | Lopata Hall, Box 1099, One Brookings | | | Drive, St Louis, Mo, 63130 | | ----------------------------------------------------------------------------- From lrellick@magnus.acs.ohio-state.edu Fri Sep 18 06:14:23 1992 Date: Fri, 18 Sep 92 10:14:23 EDT From: Lorraine M Rellick To: chemistry@ccl.net Subject: transition dipole moments and magnetic moments Dear Netters, does anyone know which software program I can use to calculate the transition dipole moments and magnetic moments for molecules containing 20-30 atoms (approx.)? Any (ANY) help will be appreciated! - Lori Rellick, Biochemistry Dept. OSU From PPANETH1@PLEARN.bitnet Fri Sep 18 11:23:26 1992 Date: Fri, 18 Sep 92 16:35:51 CET From: Piotr Subject: Mopac 6 with SCRF To: CC List Hi Everybody, I'm in desperate need of any MO package (but preferably Ampac/Amsol or Mopac 5 or 6) which has SCRF implemented for both AM1 and PM3 Hamiltonians and can be ported to either SGI, IBM 3090 or PC486 platform. Thanks in advance, Piotr ======================================================================== Dr. hab. Piotr Paneth Institute of Applied Radiation Chemistry Technical University of Lodz Zwirki 36, 90-924 Lodz, POLAND voice: (+48-42) 31-31-93 fax: (+48-42) 36-02-46 telex: 885452 ITR PL e-mail PPANETH1 \ PLEARN.bitnet (CMS) PPANETH1 \ zsku.p.lod.edu.pl (Unix) PPANETH1 \ LODZ1.DECnet (VMS) ======================================================================== From rpm@wag.caltech.edu Fri Sep 18 01:20:47 1992 Date: Fri, 18 Sep 1992 08:20:47 -0700 From: "Richard P. Muller" To: chemistry@ccl.net Subject: Mathematica modules for Brackets Has anyone written any Mathematica (or Maple, or CALC, or whatever) rules for the simplification of "brackets" matrix elements such as are found in quantum chemical energy expressions? I just started writing some, and I would be interested in what others have done along these lines. For example, if the energy of two electrons in orbital a is E = 2 + (aa,aa) and we vary a to be a+x*b, how does the energy change? E' = 2 + 4x* + (aa,aa) + 4x*(aa,ab) + ... It isn't difficult to work these expressions out, just tedious, and I'm worried that I'll make some careless errors which will later be incorporated into my programs. It should be easy to write some simple rules for Mathematica to follow. If anyone has already done something like this let me know; I will post whatever rules I finally come up with to the mlist. Thanks in advance for your time. -Rick Muller rpm@wag.caltech.edu From br1@inel.gov Fri Sep 18 16:13:42 1992 Date: Fri, 18 SEP 92 13:27:38 From: br1@inel.gov To: chemistry@ccl.net Subject: dielectric constants This is in response to a question by Bill Welsh concerning the calculation of Dielectric Constants. May I suggest John D. Ramshaw (LANL) J. Chem. Phys. 76(2) 1183, (1982) as one place to start. From jdurant@snll-arpagw.llnl.gov Fri Sep 18 06:10:44 1992 From: jdurant@snll-arpagw.llnl.gov (durant joseph) Subject: QCISD and G92 To: chemistry@oscsunb.ccl.net (Computational Chemistry) Date: Fri, 18 Sep 92 13:10:44 PDT Hello all, I am trying to run some geometry optimizations at the QCISD level using G92, but am running into troubles; the QCISD iteration counter isn't reset between each of the QCISD calculations (which presumably are calculating the analytic gradient), and I run out of iterations before the calculation is done. This iteration counter is not the one that counts geometries, but rather the steps in evaluating the QCISD energy. Is there a way to increase the maximum number of iterations in the QCISD evaluation? I tried to get around the problem by using QCISD=(conv=6), but g92 declared that to be a syntax error. My job deck looks like: ----------------------------------------------------------------------- #QCISD 6-31G* opt=(ts,grad,calchffc) NH-O (3A) transition state QCISD geometry opt. 0,3 X O, 1, 1.0 H, 2, OH, 1, 90.0 N, 2, NO, 1, 90.0, 3, 0.0 Variables: OH=1.36 NO=2.499 ----------------------------------------------------------------------- Thanks in advance, Joe Durant From chm6@midway.uchicago.edu Fri Sep 18 10:54:24 1992 Date: Fri, 18 Sep 92 15:54:24 CDT From: "Chuck M." To: CHEMISTRY@ccl.net Subject: FORTRAN-90 Dear Netters: Can anyone tell me the status of FORTRAN-90. For example, what machines have F-90 (9X) compilers or preprocessors. What packages or groups are employing F-90 presently. What are the general opinions of the new version of the language. I am partiuclarly interested in the relationship of F-90 to ab intito programs and/or packages. Thank You Charles H. Martin The Department of Chemistry and The James Franck Institute The University of Chicago chm6@quads.uchicago.edu From MCCCM@canal.crc.uno.edu Fri Sep 18 09:49:00 1992 Date: Fri, 18 Sep 1992 15:49 CST From: MCCCM@canal.crc.uno.edu Subject: Dielectric Constants To: CHEMISTRY@ccl.net Dear Netters, With respect to my last request on how to calculate the dielectric constant using MD methods I regret to say that I did not get any answer but I got several asking for the results of the inquire. We decided to use DISCOVER and run simulations using a box of 217 water molecules with periodic boundary conditions. After an interesting an tedious search of the history file we were able to locate the coordinates and velocities for each step of the simulation. There are also a huge amount of information on that file. I will be glad to hear from someone what else and in what order is the information on the history file. The manual, I have, does not contain the format on the history file. With the above information and assuming (????) that the long range forces are treated using the Ewald sum as explained in section 5.5.2 in Allen & Tildesley book I would just need to know the value of the dielectric constant of the medium surrounding the boxes inside the cutoff region. There is a dielectric constant input in the program but it seems to me that it will be used inside on the cutoff region and not outside if it is outside the problem is already solved. Can someone clear this matter for me? Bye Monica Concha Department Of Chemistry University Of New Orleans New Orleans LA 70148 Internet: mcccm@uno.edu Bitnet: mcccm@uno From twhitley@ncsa.uiuc.edu Fri Sep 18 17:34:51 1992 Date: Fri, 18 Sep 92 22:34:51 CDT From: twhitley@ncsa.uiuc.edu (Timothy A. Whitley) To: CHEMISTRY@ccl.net, chm6@midway.uchicago.edu Subject: Re: FORTRAN-90 Charles Martin asks about the status of FORTRAN 90. o FORTRAN 90 achieved the status of ANSI standard this year. o NAG markets a F90 preprocessor that translates F90 into C. o IBM and Cray Research have announced that they are developing full F90 compilers to be released next year (or so). This is all I have heard about this subject (besides details of the standard, which I won't go into here). =~=~=~=~=~=~=~=~=~=~=~=~=~=~=~=~=~=~=~=~=~=~=~=~=~=~=~=~=~=~=~=~=~= Tim Whitley, Cray Research, Inc. (( twhitley@ncsa.uiuc.edu 405 N. Mathews Avenue )) (217) 244-4863 Urbana, IL 61801 (( "These are my views only!"