From owner-chemistry@ccl.net Wed Aug 9 04:47:45 1995 Received: from chu.chem.nthu.edu.tw for ccluser@chu.chem.nthu.edu.tw by www.ccl.net (8.6.10/930601.1506) id EAA03940; Wed, 9 Aug 1995 04:43:01 -0400 From: Received: by chu.chem.nthu.edu.tw (AIX 3.2/UCB 5.64/4.03) id AA15219; Wed, 9 Aug 1995 16:43:01 +0900 Message-Id: <9508090743.AA15219@chu.chem.nthu.edu.tw> Subject: Want to know E-mail address To: chemistry@ccl.net Date: Wed, 9 Aug 95 16:43:00 TAIDT X-Mailer: ELM [version 2.4dev PL17] Dear list members, Does anybody know the E-mail address of Dr.Doug Fox? I lost his E-mail address by accident. sincerely, ===================================================================== Chiu-Ling Lin | E-mail: ccluser@chu.chem.nthu.edu.tw Department of chemistry | National Tsing Hua University | Phone: 886-35-721634 Hsinchu, Taiwan 30043 | Fax: 886-35-711082 ===================================================================== From owner-chemistry@ccl.net Wed Aug 9 07:47:47 1995 Received: from rs2.hrz.th-darmstadt.de for schulte@ws09.pc.chemie.th-darmstadt.de by www.ccl.net (8.6.10/930601.1506) id HAA05657; Wed, 9 Aug 1995 07:43:42 -0400 Received: from ws09.pc.chemie.th-darmstadt.de by rs2.hrz.th-darmstadt.de with SMTP id AA16409 (5.65c/IDA-1.4.4 for ); Wed, 9 Aug 1995 13:43:09 +0200 Received: by ws09.pc.chemie.th-darmstadt.de (AIX 3.2/UCB 5.64/4.03) id AA13102; Wed, 9 Aug 1995 13:43:45 +0200 From: schulte@ws09.pc.chemie.th-darmstadt.de (Joachim Schulte) Message-Id: <9508091143.AA13102@ws09.pc.chemie.th-darmstadt.de> Subject: SUMMARY: Mopac 7.0 and symmetry To: chemistry@ccl.net Date: Wed, 9 Aug 1995 13:43:44 +0200 (CST) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 1021 Dear Ladies and Gentlemen, my problem was that Mopac 7.0 did not recognize some point groups correctly, namely IH and D5H. Dr. James Stewart and Dave Close both recommended to switch to MOPAC 93 for doing routine calculations. MOPAC 7.0 indeed has problems recognizing the point groups of many systems. Dr. Stewart writes: ''MOPAC 7 was not designed to recognize C60. MOPAC 7 was limited to systems for which the principal axis is either perpendiculer to a set of atoms (Benzene) or goes through some of the atoms. In C60, the principal axis is through the middle of a pentagon. For routine use, MOPAC 93 is recommended over MOPAC 7. MOPAC 93 will recognize C60 as being Ih, and a whole slew of weird and wonderful systems - truncated icosahedra (like C60), truncated cubes and tetrahedra, and `twisted' icosahedra (point-group `I')...'' So I will switch to MOPAC 93 for my calcluations on fullerene systems. Many thanks to Dave Close and Dr. Stewart. Sincerely Yours, Joachim Schulte From owner-chemistry@ccl.net Wed Aug 9 08:32:48 1995 Received: from scripps.edu for rickr@scripps.edu by www.ccl.net (8.6.10/930601.1506) id IAA06013; Wed, 9 Aug 1995 08:31:59 -0400 Received: from aries.scripps.edu by scripps.edu (5.61/1.34) id AA25159; Wed, 9 Aug 95 05:31:58 -0700 Received: by aries.Scripps.EDU (4.1/SMI-4.1) id AA25019; Wed, 9 Aug 95 05:31:50 PDT Date: Wed, 9 Aug 95 05:31:50 PDT From: rickr@scripps.edu (Rick Ross) Message-Id: <9508091231.AA25019@aries.Scripps.EDU> To: chemistry@ccl.net Subject: running MOPAC93-revision 2 on SGI Hi Folks, I was wondering if anyone has been successful in compiling, linking, and running MOPAC93 - Revision 2 on SGI workstations. With the help of some other folks (thanks!) I have been able to compile and link the program. However, when I run the program (for ethylene for example), instead of getting numbers for heats of fomration, etc., I get "nan". I understand from an SGI very helpful person that "nan" means "not a number" and is indicative of a serious mathematical problem. Has anyone else seen this behavior? Is anyone succesfully running MOPAC 93 - Revision 2 on SGI? Does anyone have a make file they would be willing to share or have a way to correct the "nan" problem? Thanks in advance for any replies. I would be glad to share the results with the list if there is interest. with best regards, Rick Ross PPG Industries P.O. Box 9 Allison Park, PA 15101 email: rickr@ppg.scripps.edu voice: (412) 492-5359 FAX: (412) 492-5577 From owner-chemistry@ccl.net Wed Aug 9 09:32:53 1995 Received: from phem3 for PA13808@UTKVM1.UTK.EDU by www.ccl.net (8.6.10/930601.1506) id JAA06997; Wed, 9 Aug 1995 09:31:25 -0400 From: Received: from UTKVM1.BITNET (MAILER@UTKVM1) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HTV4TO6X1C9CN9OK@phem3.acs.ohio-state.edu>; Wed, 9 Aug 1995 09:31:17 EDT Received: from UTKVM1.UTK.EDU (PA13808) by UTKVM1.BITNET (Mailer R2.10 ptf000) with BSMTP id 6043; Wed, 09 Aug 95 09:30:43 LCL Date: Wed, 09 Aug 95 09:20:53 LCL Subject: MVSVERSION OF G92 To: chemistry@ccl.net Message-id: <01HTV4TO6X1E9CN9OK@phem3.acs.ohio-state.edu> Content-transfer-encoding: 7BIT Our systems group are still trying to install G92 revision G on our MVS IBM system. Apparently IBM not Gaussian are supposedly responsible for supplying the correct load module or instructions but they have not come through with anything we can use.Has anyoone out there go t one we could use. We are expecting to have a unix copy of G94 installed on a unix workstation very soon but still like to use the more powerful MVS system as well as long as we have it available. Help!! John E. Bloor(PA13808 at utkvm1.utk.edu) From markz@chem.duke.edu Wed Aug 9 16:33:03 1995 Received: from duke.cs.duke.edu for markz@chem.duke.edu by www.ccl.net (8.6.10/930601.1506) id QAA15151; Wed, 9 Aug 1995 16:29:45 -0400 Received: from london.chem.duke.edu by duke.cs.duke.edu (5.65/3.10G/4.1.3) id AA04805; Wed, 9 Aug 95 16:29:38 -0400 Received: from dna.chem.duke.edu by london.chem.duke.edu (5.64/1.19LP/4.1.1) id AA16276; Wed, 9 Aug 95 16:29:37 -0400 Received: by dna.chem.duke.edu (5.64/2.12L/4.1) id AA18223; Wed, 9 Aug 95 16:29:36 -0400 Date: Wed, 9 Aug 1995 16:29:36 -0400 (EDT) From: "Mark A. Zottola" To: chemistry@ccl.net Subject: Conformational Analysis Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Is there a gold standard for exhaustively searching conformational space for discrete conformers? I realize that there is systematic search (but this fails for large and floppy molecules). I can imagine using distance geometry as a source for exhausting conformational space as well. Is there a concensus on a method? I would prefer public domain or QCPE-available code as opposed to "professional" efforts. If there is sufficient interest, I will summarize to the list. Thanks! -Mark ****************************************************** * * * * * Mark A. Zottola * * markz@dna.chem.duke.edu * * Department of Chemistry * * Duke University * * Durham, NC 27704 * * * * * * The fault, dear Brutus, lies not with ourselves, * * but rather within our CPUs. * * (with apologies to Shakespeare * * * * * ****************************************************** From mrigank@imtech.ernet.in Wed Aug 9 16:47:55 1995 Received: from sangam.ncst.ernet.in for mrigank@imtech.ernet.in by www.ccl.net (8.6.10/930601.1506) id QAA15410; Wed, 9 Aug 1995 16:41:46 -0400 Received: (from uucp@localhost) by sangam.ncst.ernet.in (8.6.12/8.6.6) with UUCP id CAA20870 for chemistry@ccl.net; Thu, 10 Aug 1995 02:12:13 +0530 Received: from imtech.UUCP by doe.ernet.in (4.1/SMI-4.1-MHS-7.0) id AA21113; Thu, 10 Aug 95 01:59:42+050 Message-Id: <9508092059.AA21113@doe.ernet.in> Received: by imtech.ernet.in (DECUS UUCP w/Smail); Wed, 9 Aug 95 22:48:19 +0530 Date: Wed, 9 Aug 95 22:48:19 +0530 From: Mrigank To: chemistry@ccl.net Subject: Cl parameters ? I am doing some simulations which includes a molecule containing Chlorine. Can any one suggest NB, angle and dihedral angle parametrs for it. For anlgels it is attached to a benzene ring substituting hydrogen. I would appreciate parameters that will go with AMBER 91 or OPLS force field. Thanks in advance mrigank ---- /Mrigank \/ Phone +91 172 690557 \ \Institute of Microbial Technology /\ Email: mrigank@imtech.ernet.in / /Sector 39A, \/ FAX: +91 172 690585 \ \Chandigarh 160 014 India. /\ / \//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\// -- When I feed the poor, they call me saint. When I ask why the poors do not have food, they call me communist - Archbishop Camaran From shenghua@iris54.biosym.com Wed Aug 9 19:32:56 1995 Received: from bioc1.biosym.com for shenghua@iris54.biosym.com by www.ccl.net (8.6.10/930601.1506) id TAA17255; Wed, 9 Aug 1995 19:23:44 -0400 Received: from iris54.biosym.com by bioc1.biosym.com (5.64/0.0) id AA20420; Wed, 9 Aug 95 16:22:14 -0700 Received: by iris54.biosym.com (940816.SGI.8.6.9/930416.SGI) for CHEMISTRY@ccl.net id QAA08625; Wed, 9 Aug 1995 16:22:18 -0700 Date: Wed, 9 Aug 1995 16:22:18 -0700 From: shenghua@iris54.biosym.com (Shenghua Shi ) Message-Id: <199508092322.QAA08625@iris54.biosym.com> To: CHEMISTRY@ccl.net Subject: CCL:summary of responses about esff >Received: by HUJIVMS (HUyMail-V7b); Mon, 07 Aug 95 17:14:59 +0200 >Received: by HUJIVMS (HUyMail-V7b); Mon, 07 Aug 95 17:07:09 +0200 >Date: Mon, 7 Aug 95 17:06 +0200 >Message-Id: <07080095170658@HUJIVMS> >From: >To: chemistry@ccl.net >Subject: CCL:summary of responses about esff >Sender: Computational Chemistry List >Errors-To: ccl@ccl.net >Precedence: bulk > >hi, >>This is the summary of answers i got about the >esff force field. > > ESFF is an Extensible and Systematic Forcefield developed at Biosym for molecular modeling of organic, inorganic, and organometallic systems. It covers all the elements in the periodic table up to Rn. Currently, ESFF is able to predict structures of isolated molecules as well as systems of condensed phases. In addition, it can be used to predict properties related to non-bonded interactions, such as sublimation energies, with reasonable accuracy. In the upcoming Discover release, systems treated by ESFF can have up to 10000 atoms per unit cell. Thanks to input from many of our customers, ESFF has improved considerably since its first (beta) version which was released a year ago. The preliminary results of a number of in-house and customer applications indicate that ESFF reproduces experimental structures fairly well for a variety of systems including nucleic acids, porphyrins, transition metal complexes, and organometallic compounds. The following is a brief summary of the ESFF methodology: ESFF is a diagonal valence forcefield. The valence bond, angle, torsion, and out-of-plane energies are used to describe the internal interactions, while Van Der Waals (VDW) and electrostatic energies represent the non-bonded interactions. In many systems, specifically metal complexes, deviations in bond lengths and bond angles from equilibrium geometries are large. To account for this fact and the periodicity of angle energies in coordination compounds, we have implemented Morse functions for bond energies and truncated cosine series for angles energies. A novel functional form is used to describe the torsion energies. It is essentially an entire function of dot products of unit vectors. This type of function insures that there is no singularity when the bond angles approach 180 as well as significantly simplifies the calculation of the Cartesian derivatives of the torsion energies. Moreover, the parameters in the VDW energy terms, like the electrostatic term, are products of single atomic quantities. The advantage of such expressions is that the nonbond energy can be computed more efficiently using advanced techniques such as the Cell Multipole method or methodologies based on Fast Fourier Transform. The forcefield parameters are generated from atomic parameters based on rules that embody the physics of atom-atom interactions. The number of atomic parameters scale as a linear function of the total number of atom types. Although, this approach has been used in the past, the rules have been too general to yield a forcefield with sufficient accuracy. We have extended the philosophy of the approach in several ways to improve the accuracy and parameter transferability: 1) We have augmented the specificity of atom types with the inclusion of internal type classification to capture detailed behaviors associated with particular internals. The atomic parameters depend not only on the atom types but also the internal types. This allows for a more accurate representation of constrained systems, conjugated systems, dative effect (due to sigma lone pair - vacant orbital interaction), pi dative effect (resulting from pi lone pair-vacant orbital interaction), electron back donating effect, and Jahn-Teller effect. 2) By introducing a concept of pseudo-angles, the ESFF forcefield can reproduce unconventional structures resulting from d-p pi bonding between the unsaturated ligands and transition metals. 3) Many of the rules used in ESFF have been derived from approximate models which grasp the essense of the underlying physics. These rules have enabled us to produce a relatively small set of physically meaningful and transferable parameters. For example, by combining London's formula for dispersion energy with a harmonic oscillator model for the polarization, semiempirical expressions for the VDW radii and well depth have been derived. The expressions represent such a good correlation that more than a thousand VDW parameters for all atom types are generated from as few as ~30 atomic parameters. 4) Considering the complexity of the physics involved in atomic interactions, we have derived schemes to use a series of rules instead of a single rule in order to account for various critical effects. For example, the partial atomic charges are calculated using an elaborated scheme whereby atoms are grouped into different charge groups according to their bonding nature. Depending on the group, the partial charges are determined using different algorithms derived from either the group electronegativity equalization or the local electronegativity equalization (for a pair of bonded atoms). The scheme also takes into account the inductive, resonance and field effects in the different stages of calculation. 5) We have developed a unique algorithm to generate the fundamental atomic parameters, such as electronegativity, hardness and ionization potential for all atom types (ie. atoms having different hybridizations, oxidation numbers, coordination numbers or symmetries) by making use of the density functional theory. A more detailed description of ESFF parameterization is available on request. The development and enchancement of the ESFF forcefield is a continuous effort at Biosym. Therefore, we gladly welcome feedback from our users. Please do not hesitate to contact our response center or me if you have any questions or comments regarding ESFF. Thanks, shenghua ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Shenghua Shi BIOSYM Technologies shenghua@biosym.com 619-546-5348 From rosas@irisdav.chem.vt.edu Wed Aug 9 20:33:05 1995 Received: from irisdav.chem.vt.edu for rosas@irisdav.chem.vt.edu by www.ccl.net (8.6.10/930601.1506) id UAA17741; Wed, 9 Aug 1995 20:30:54 -0400 Received: by irisdav.chem.vt.edu (940816.SGI.8.6.9/940406.SGI) for chemistry@ccl.net id UAA16723; Wed, 9 Aug 1995 20:26:02 -0400 From: "Victor M. Rosas Garcia" Message-Id: <9508092025.ZM16721@irisdav.chem.vt.edu> Date: Wed, 9 Aug 1995 20:25:59 -0400 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@ccl.net Subject: Summary of minimization w/COSMO Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi there, Sorry this summary is a little late. My original posting was: ________________________________________________________________________________ Hi CCL'rs, I'm currently minimizing some molecules in MOPAC93, using a dielectric constant of 78.3. Mi starting point is the structure optimized in gas phase using MOPAC 6.0. After the run is finished I get the message: "THE LINE MINIMIZATION FAILED TWICE IN A ROW. TAKE CARE!" And the GRADIENT NORM varies between 2 and 25 (a little too high, I think). This are the keywords I'm using: AM1 EPS=78.3 NOINTER T=3600.00 PRECISE I have looked up in the list of error messages provided in the MOPAC 93 manual but the message is not there. Is this something to be concerned about? Should I be concerned about the gradient norm? Any help will be appreciated. ________________________________________________________________________________ I received a few answers, and basically the recommendations were: 1) Take the output geometry and use it as input for another run. (I have done it and it usually works, but it can be tedious at times) 2) Use EF instead of BFGS and specify GNORM=0.01 3) Use keywords NODIIS and XYZ 4) Modify the code to stop after the average deviation of the delta Hf over the last five cycles is < 0.1 Kcal 5) In addition to EF, specify LET and DDMIN=0.0 6) Perturb one of the original parameters, let's say stretch a bond length by 0.15 ang so that the optimizer will have a chance to get a good Hessian. 7) Do not be concerned about the gradient norm as long as it is less than 2. Thanks to the CCL and specially to: Jaime Combariza Steve Bowlus Andrew T. Pudzianowski John McKelvey Stanislaw Oldziej and Dave Giesen Victor PS. Somehow I think I'm missing ONE name. I can't find it. Sorry. From rosas@irisdav.chem.vt.edu Wed Aug 9 21:03:05 1995 Received: from irisdav.chem.vt.edu for rosas@irisdav.chem.vt.edu by www.ccl.net (8.6.10/930601.1506) id VAA17950; Wed, 9 Aug 1995 21:00:53 -0400 Received: by irisdav.chem.vt.edu (940816.SGI.8.6.9/940406.SGI) for chemistry@ccl.net id UAA16921; Wed, 9 Aug 1995 20:56:00 -0400 From: "Victor M. Rosas Garcia" Message-Id: <9508092055.ZM16919@irisdav.chem.vt.edu> Date: Wed, 9 Aug 1995 20:55:56 -0400 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@ccl.net Subject: Negative freq. for ground state??? Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi CCL'rs, It's me again :) I've got a weird problem with MOPAC 93. I trying to calculate free energies of solvation for several sets of conformers (no TS's involved). This involves calculating the frequencies and principal moments of inertia for each conformer, both in gas phase and in solution, to account for the entropic contribution to the free energy. I'm using FORCE for this, but every now and then I get a *negative* frequency even though there are no negative force constants in the force matrix. The problem is more frequent when I use FORCE and EPS=78.3, but it does appear for the gas phase calculations too. Usually there will appear one negative frequency with an absolute value less than 40 cm^-1 (sometimes two). FORCE found the gradients to be acceptable (<2) in all cases so no additional minimization was done by FORCE. According to the manual (regarding TS optimization) there is a way to get rid of spurious negative frequencies which is to run a DRC along the spurious mode. However, when I use Cerius2 to animate the negative frequency mode I see that it is quite complex. Basically all the atoms move, so it is not obvious to me how I can define a DRC along so many coordinates. BTW, the molecules I'm working on are either zwitterions or tetraalkylammonium cations (carnitine and choline). To make it brief my main questions are: 1) Is it possible to have a negative freq. and no negative force constant? 2) what meaning can be attached to a negative frequency (if any)? 3) Does it make sense to run FORCE and EPS=78.3 together? 4) Am I missing something really simple here? Thanks in advance. Victor -- ------------------------------------------------------------------------- Victor M. Rosas Garcia * "How can we contrive to be rosas@irisdav.chem.vt.edu * at once astonished at the Virginia Tech doesn't necessarily share * world and yet at home in it?" the opinions you just read. * G. K. Chesterton -------------------------------------------------------------------------