From chemistry-request@server.ccl.net Mon Jan 21 11:13:04 2002 Received: from guppy.vub.ac.be ([134.184.129.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0LGD3I25689 for ; Mon, 21 Jan 2002 11:13:04 -0500 Received: from mach.vub.ac.be (mach.vub.ac.be [134.184.129.3]) by guppy.vub.ac.be (8.9.1b+Sun/3.17.1.ap (guppy)) id RAA05830; Mon, 21 Jan 2002 17:12:15 +0100 (MET) for Received: from vub.ac.be (algcpc5.vub.ac.be [134.184.24.95]) by mach.vub.ac.be (8.9.3/3.13.3.ap (mach)) id RAA29852; Mon, 21 Jan 2002 17:12:34 +0100 (MET) for Message-ID: <3C4C3E63.6080405@vub.ac.be> Date: Mon, 21 Jan 2002 17:14:27 +0100 From: Pierre Mignon User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; rv:0.9.4) Gecko/20011128 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: chemistry@ccl.net Subject: FF, and QM/MM Software Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hello everybody, I am interested to buy a software to do QM/MM calcculations and FF minimalisations for a project concerning biochemistry. I know some about CHARMM or AMBER, but I have never use them. Could anybody give me suggestions and critics upon their use and also on other software ? Thank's in advance. Pierre Mignon . From chemistry-request@server.ccl.net Sun Jan 20 13:52:16 2002 Received: from dqf.ufpe.br ([150.161.5.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0KIqFI22671 for ; Sun, 20 Jan 2002 13:52:15 -0500 Received: from npd.ufpe.br ([150.161.5.215]) by dqf.ufpe.br (8.11.4/8.11.4) with ESMTP id g0KHxWo06767 for ; Sun, 20 Jan 2002 15:59:32 -0200 Message-ID: <3C4B116A.FD163B6C@npd.ufpe.br> Date: Sun, 20 Jan 2002 16:50:18 -0200 From: Bosco X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Program for calculating rotational levels? Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear colleague, Please, I am looking for a program calculating rotational levels of top assymetric molecules. Any information is welcome! Thanks in advance, Bosco -- Prof. João Bosco Paraiso da Silva e-mail: paraiso@npd.ufpe.br Bosco´s Homepage: www.dqf.ufpe.br/professores/bosco/bosco.html Departamento de Química Fundamental Universidade Federal de Pernambuco 50740.250 - Recife (PE) - Brazil DQF´s Homepage: www.dqf.ufpe.br Phone: +55 81 3271-8441 ext. 5009 Fax: +55 81 271-8442 From chemistry-request@server.ccl.net Mon Jan 21 09:25:48 2002 Received: from MAIL.AD.Berry.edu ([66.20.28.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0LEPlI23500 for ; Mon, 21 Jan 2002 09:25:47 -0500 Received: from [10.16.232.24] ([10.16.232.24]) by MAIL.AD.Berry.edu with Microsoft SMTPSVC(5.0.2195.2966); Mon, 21 Jan 2002 09:26:44 -0500 User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 Date: Mon, 21 Jan 2002 09:25:32 -0500 Subject: SUMMARY: Question pertaining to Vibrational Frequencies From: Gary Breton To: CC: , , , , Message-ID: Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit X-OriginalArrivalTime: 21 Jan 2002 14:26:44.0643 (UTC) FILETIME=[A6D64730:01C1A287] Hello, Thank you so much for all of your responses to my question on vibrational frequencies. The original question is given below: I performed a minimization on a structure using Gaussian 98W (B3LYP/6-311+G**) and followed it up with a frequency calculation at the same level (of course). I obtained a single negative frequency at -27cm-1. I then re-optimized the geometry at the same level but this time ignored symmetry. The new E was lower than the previous by 0.03 kcal/mol. The newfrequency calculation afforded a single negative frequency at -11 cm-1. David Young's "Computational Chemistry" book suggests (page 94) that frequency values with a range of about -20 to 20 cm-1 are essentially zero within the numerical accuracy of most software packages. Is this true for G98 as well? > To sum it all up: Can I take a -11 cm-1 frequency to be inconsequential? or do I need to continue to play with the system until absolutely no negative frequencies are present? I had many requests for a summary of the answers. I provide these below without the names of those responding (which I guess is good etiquette, could be wrong). My final solution? still working on it. I think that my final take home message is the following: small negative frequencies suggest that you are close to a minimum. Probably the energy at this point is NOT very different than the energy at the minimum that you are close to. However, one should do what one can to eliminate this minimum. Suggestions for doing this are given below. Thanks again and best regards to the group members! ****************************************************** A frequncy of -11 cm-1 is a transition state. However, I suspect that your case is "undecided". The number of imaginary freqs gives the curvature of the PES at the stationary point in question. G98 thinks that at your stationary point, with the method (B3LYP) and basis set (6-311+G**) you used the PES is mildly saddle-shaped, but not very different from a minimum. Another method/basis might give a distinct saddle or minimum. Borderline cases like this could require high computational levels to settle. *************************** This imaginary frequency should disappear! To my knowledge, this is not a problem of minimisation. May be you have a methyl group in your molecule that in badly oriented. Just changing its orientation is OK! **************************** I wouldn't worry about a single imaginary frequency as low as 11i cm**-1. It is so low (there's about 350 cm**-1 to a kcal/mole!) that it may well be caused by numerical noise from the integration. You could try integrals(grid=ultrafine) to see if it goes away, but as I said, it doesn't really matter. **************************** One of the most important things to look at, is the six lowest eigenvalues of the Hessian (or frequencies) in absolute sense. In an ideal world, where the QuantumChemical packages would be able to provide geometries with exactly zero gradients, these lowest six should all be zero. The fact that they are not in practice, is (among other factors maybe) due to the fact that the gradient is not exactly zero, but below a certain threshold. Therefore, if your -11 cm-1 is one of these six lowest frequencies, then you can ignore it. NOTE: Gaussian used to be one of the packages that would already filter the output, i.e. the six lowest frequencies were not displayed in the list of frequencies, as I seem to remember. However, at another place in the output, they were displayed. As I haven't done frequency calculations with Gaussian for a few years now, I'm not sure if this is (still) true. Just be careful. ***************************** In my opinion, the small imaginary frequency can be looked as an error > from computation and it is difficult to avoid for some systems. But maybe it is a rotational excited state as well. So please try to change your structure according to the imaginary frequency to find if you can get rid of it. Of course you may try opt=tight, too. ******************************* You are going to get a lot of responses saying the same thing: YES, a freq of -11 may be taken as zero and does not mean you have a saddle. I have done dozens of freq calcs via Gaussian98 at geoms optimized at the B3LYP/6-311++g** level and I usually get anywhere from one to 5 just barely negative frequencies. Perhaps more to the point, when it has been a t-state, the negative freq has always been < -100. ******************************* While a small value like -11cm-1 can arise from a couple of sources I would not suggest you pass it off, especially if it is a mode which would have bearing on any of the chemistry you wish to describe. On the other hand I would agree that making any prediction about the observed frequency of a mode less than 20 wavenumbers based on this calculation is not warranted. So I will make a couple of general comments and help you see the next step. First, there is are two sets of "Frequencies listed" the "low frequencies" and then the normal mode listings including intensities, reduced masses etc. The latter can be given twice if you used the HPmodes option. The first set are the lowest 10 modes from diagonalizing the full 3Natoms by 3Natoms matrix and so there will be 6 low frequency modes, say under 10 wavenumbers and they correspond to overall rotation and translation. Negative values at this point for these modes is not particularly worth note. Then this matrix has the analytic rotation and translation modes projected out and the remaining 3NAtoms-6 modes are determined. At this point only vibrations are left and negative frequencies of any size are harder to dismiss. Second, even with NoSymm you can end up with a symmetric structure because the gradient carries the symmetry of the structure and will not follow anti-symmetric modes downhill. So if the negative frequency is not totally symmetric, i.e. is anything except A1 symmetry, you may only have gotten numerical noise in the re-optimization. Re-optimizing to break the symmetry also requires moving the structure along to lower symmetry, best by displacing along that mode. You can add the displacement vector from the FREQ analysis element by element to the structure. Third, DFT does have more of a problem with numerical precision because of numerical integration. With a low frequency mode like this I have seen use of Int=Grid=UltraFine or one of the higher order angular grids, see the Int keyword, clean up the integration. You would need to use OPT=ReadFC with this Grid followed by FREQ with this same grid to be sure you have it. If your negative frequency is on the Low Freq list and not a normal mode, you are likely fine and it is just numerical. If the structure really is reported as C1 then this may well be real and you should go on to use a better integration grid to sort it out. Or if the structure is still rated as symmetric and this mode breaks symmetry try breaking the symmetry and re-doing the optimization at the lower symmetry. Agreed that modes this low are not going to make large energy differences but if it is a dihedral it can result in opening up a structure by a few degrees, enough to change conclusions. ***************************** i am by no means an expert, but during my calculations on the same level of theory, i had the same problem. what this imaginary freqency means is essentially that you have a very flat poteential energy surface and there are probably more structures to explore. so what you should do is alter the structure and perform a new minimization and see where it takes you. ******************************* You can probably ignore this frequency. Some energy surfaces are fairly flat (especially when a molecule can undergo internal rotations), and frequency calculations "reveal" imaginary frequencies even when you have effectively optimized the geometry. But just to be sure, you might try the following - if the calculation is convenient to do, you could tighten the optimization criteria and repeat the geometry optimization + frequency calculation. (Sorry, but I don't know how you specify these criteria in Gaussian). ******************************** >To sum it all up: Can I take a -11 cm-1 frequency to be inconsequential? Yup. or >do I need to continue to play with the system until absolutely no negative >frequencies are present? Nope. > > as you can see in your example the amount of additional stabilization left in these soft modes is pretty minimal and thus is not worth chasing. *********************************** I prefer to tighten the SCF and the opt convergence criteria, use calcfc, and so on to see if I can remove such -ve frequencies. This can waste a lot of time though, and sometimes you never get rid of them, so you accept you're as close to the minimum as you're going to get. I've had more numerical trouble with DFT than HF/MP*. The -11 is a bit of a problem if you want to use and compare the ZPE and thermochemistry. ********************************** I, too, am uncomfortable with small imaginary frequencies. With the standard HF methods, one could usually rewrite the z-matrix to better represent the internal coordinates to get rid of them or "nudge" the internal coordinate(s) for the imaginary freqs and re-optimize. However, for DFT methods, these tactics are not highly reliable. Nowadays, people (including myself) tend write the input in terms of xyz coordinates and let G98 decide on the redundant internal coordinates so modifying the internal coordinates are a bit more tricky. One possible solution is just to re-order the xyz coordinates (especially the first 3) so that G98 will re-orient the molecule differently in space. Since DFT is a grid-based methods, this "coordinate juggling" procedure will very slightly alter the gradients that are being computed so that in the long run your freqs will all turn out real (hopefully, 8^) ). Of course, this leads to the second solution which is to simply add the option "int=ultrafine" which will give you a finer grid for the DFT calculation. This solution will result in greater CPU time (dependent on size of molecule), but it keeps you > from having to "play games" to get rid of the imaginary freqs. ************************************ Try opt=tight. *********************************** I have heard (second hand from Gaussian) that up to about -50 cm-1 may be considered effectively zero. The problem is more acute with DFT methods compared to Hartree-Fock or post HF methods since the DFT calculations have greater accumulation of rounding errors due to the numerical integration that is required. ************************************** Are you using the ultrafine grid? Try if you are no using!! And maybe this frequency will desapear! From chemistry-request@server.ccl.net Mon Jan 21 10:46:51 2002 Received: from mail.fqspl.com.pl ([212.244.147.7]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g0LFkoI25148 for ; Mon, 21 Jan 2002 10:46:50 -0500 Received: (qmail 1680 invoked from network); 21 Jan 2002 15:46:29 -0000 Received: from magda.fqspl.com.pl (HELO magda) (10.10.10.32) by fqspl.com.pl with SMTP; 21 Jan 2002 15:46:29 -0000 Message-ID: <054e01c1a292$d18bce90$200a0a0a@fqspl.com.pl> Reply-To: "FQS Poland" From: "FQS Poland" To: Subject: MOPAC 2002 for Linux. Unix, Windows Date: Mon, 21 Jan 2002 16:46:40 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6700 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 MOPAC 2002 for Linux (with GUI), Unix, Windows ============================================ * New method PM5 - 4x more accurate (over PM3 and AM1) * Addition of AM1-d - the full set of metals that can be run using AM1 is now V, Fe, Cu, Mo, Pd, Ag, and Pt. * Linear scaling COSMO * Improved SCF convergence in MOZYME * Improved evaluation of canonical molecular orbitals * Addition of new parameter sets * Molecular Mechanics correction for carbon ring systems To learn more, please visit http://www.fqspl.com.pl/linmopac/default.html ============================================= CAChe WS Pro 5.0 for Win/Mac with MOPAC 2002 ============================================= * Spreadsheet workbook for molecule properties * Quantum chemistry on giant molecules (up to 20,000 atoms) * All main group elements in one semiempirical method * A protein sequence editor * Ease of navigation through tens of thousands of atoms * Integrated QSAR and QSPR for ADME, LogP, Rule-of-5 To learn more or get a free evaluation CD with full version, please visit http://www.CACheSoftware.com/cache5 Magdalena Wilczewska Tel.: (+48 12) 429 43 45 From chemistry-request@server.ccl.net Sun Jan 20 20:43:53 2002 Received: from dns.sce.tsinghua.edu.cn ([166.111.18.14]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0L1hqI01669 for ; Sun, 20 Jan 2002 20:43:52 -0500 Message-Id: <200201210143.g0L1hqI01669@server.ccl.net> Received: from denny ([166.111.27.50]) by dns.sce.tsinghua.edu.cn (Netscape Messaging Server 3.01) with SMTP id 267; Mon, 21 Jan 2002 09:22:22 +0800 Date: Mon, 21 Jan 2002 9:46:44 +0800 From: Denny To: "WANG, YIXUAN " CC: "chemistry@ccl.net" Subject: Re: about size-consistent method Organization: Tsinghu University X-mailer: FoxMail 3.0 beta 1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit the interaction at 1nm include BSSE correction with CP method. And ZPE is not considered. How to do ZPE correction? Do frequency analyze at every single point then add the ZPE contribution to the potential energy curve? But with DFT calculation, the curve is very straight when R>0.8nm and the energy got by B3LYP is just below the dissociation limit(dissociation energy calculated from the equilibrium position). However CCSD(T),CCSD and QCISD(T),QCISD calculated energy at R=1nm is 0.5-0.8eV above dissociation limit calculated by themselves. if calculate R larger than 1nm such as 10nm, the energy will be larger also than the dissociation limit(the value will >1eV I think). Then the dissociation energy should use E(AB)-E(A)-E(B) or E(AB,R=1nm)-E(AB,R=equilibrium)? If this is due to other incomplete correction, but my calculation of CCSD(T) and QCISD(T) etc. is in very consistent with DFT calculation, for example bond length, dissociation energy, harmonic frequency. Is this the demerit of this kind of post-hf methods? for example the calcualted correlation energy is not accurate enough at large distance? I think MCSCF and MRCI calculation may avoid this. Compared with post-HF methods, I think DFT is more competent for PES of complexes of transition heavy metal element. Denny ********You wrote********* >did you make BSSE and ZPE corrections for the calculation > E(AB,nuclei distance R=1nm)-E(A,R=1nm)-E(B,R=1nm)? >I guess 0.8 ev difference may be due to your incomplete >corrections or something else rather than non-consistence >of CCSD(T). As well, to be mentioned is that AB perhaps >still considerably interact at R=1nm ( I think you test >10nm ! at least 5nm ). Hope it helps you. > > >Yixuan Wang > >-----Original Message----- >From: Denny [mailto:dilys98@mails.tsinghua.edu.cn] >Sent: Saturday, January 19, 2002 9:16 PM >To: chemistry@ccl.net >Subject: CCL:about size-consistent method > > >Dear all, > >Can someone comment something on size-consistent method? For example, I >calculated potential energy curve for molecule AB >with B3LYP,CCSD(T) and QCISD(T) methods and aug-cc-pvtz even aug-cc-pvqz, >the interaction including BSSE correction >E(AB,equilibrium position)-E(A,equilibrium)-E(B,equiblibrium) is -6.5eV, and >E(AB,equilibrium)-E(A,single body)-E(B,single >body) is also about -6.5eV. However E(AB,nuclei distance >R=1nm)-E(A,R=1nm)-E(B,R=1nm) is not 0eV but 0.8eV. Then the real >calculated dissociation energy is 6.5eV or (6.5+0.8)eV? I found CCSD(T) and >QCISD(T) is also size-inconsistent though >someone say CCSD(T) is size-consistent. > >Any comments will be welcome!!! > >Best Regards, >Denny Chen > From chemistry-request@server.ccl.net Mon Jan 21 12:10:31 2002 Received: from mail.unito.it ([130.192.119.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0LHAUI27364 for ; Mon, 21 Jan 2002 12:10:30 -0500 Received: from unito.it ([127.0.0.1]) by mail.unito.it (Netscape Messaging Server 4.15) with ESMTP id GQAT1300.IFJ for ; Mon, 21 Jan 2002 18:10:15 +0100 From: "Mssc Mssc" To: chemistry@ccl.net Message-ID: <7d4017f264.7f2647d401@unito.it> Date: Mon, 21 Jan 2002 18:10:15 +0100 X-Mailer: Netscape Webmail MIME-Version: 1.0 Content-Language: en Subject: MSSC2002 - Modeling in Solid State Chemistry X-Accept-Language: en Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g0LHAVI27365 European Summerschool Ab initio Modeling in Solid State Chemistry MSSC2002 http://www.chimifm.unito.it/teorica/mssc2002 September 8-13, 2002 -Torino, Italy Director: R. Dovesi, University of Torino The Theoretical Chemistry Group of the Torino University is organizing a Summer School on the ab initio simulation of crystalline and defective solids. The school is addressed to PhD students with interests in solid state chemistry, physics, materials science, surface science, catalysis and will provide an overview of the possibilities offered by ab initio quantum mechanical techniques when applied to characterize solid state materials. The new capabilities of the CRYSTAL code will be illustrated. Outline of the subjects * Introductory lectures: + Space groups and point symmetry + Reciprocal space and Bloch functions + Hamiltonians and Basis sets * The structure of the CRYSTAL code: basis set, hamiltonians, accuracy. * Total energy and related quantities: equations of state, solid state reactions, phase transitions. * Geometry optimization: strategies and techniques. * One electron properties: DOS, band structure, charge and spin density maps, electrostatic potential, spontaneous polarization. * Spin polarized solutions: ferromagnetism and antiferromagnetism, Fermi contact and hyperfine coupling constants. * Surface chemistry and heterogeneous catalysis: models, accuracy and limitations. * Local defects in solids: the observables of interest; the possible strategies. * Localized crystalline orbitals - Wannier Functions. * Post-HF ab initio techniques for crystals. Teachers The local staff of the Theoretical Chemistry Group (R. Dovesi, C. Pisani, C. Roetti, P. Ugliengo, S. Casassa, A. Ferrari, B. Civalleri, F. Lopez, I.P.R. de Moreira, Y. Noel, M. Busso, A. Damin, G. Mallia, F. Pascale from Torino University and R. Orlando from the University of Eastern Piedmont) will be supported by highly qualified European scientists, including: M. Catti, Università di Milano Bicocca (Milano) - Italy F. Corà, The Royal Institution (London) - U.K. Ph. D'Arco, Université P. et M. Curie (Paris) - France E. Giamello, Dipartimento Chimica IFM (Torino) - Italy N. M. Harrison, CLRC and Imperial College - U.K. V. R. Saunders, CLRC Daresbury Laboratory - U.K. A. Savin, Université P. et M. Curie (Paris) - France C. M. Zicovich Wilson (Cuernavaca) - Mexico Program The school will last six days (8-13 September 2002) and will be held at the Chemistry Departments of the Torino University. The morning sessions will be devoted to lectures by experts. The afternoons will be dedicated to practical sessions. In the tutorials it will be shown how to obtain information concerning various observables using the CRYSTAL code. There will be the possibility to present posters, that will be on display for the whole school and discussed during a special session. Participation is limited to 40 people. Accommodation will be at the University guest house, in double rooms. The total cost of the school is expected to be 450.00 Euro. A small number of bursaries will be available, to cover the participation fee of researchers from less favourite countries. Deadlines and Contact Information: II circular and application form: March 15th Submission of application form: May 1st Notification of acceptance: May 15th Submission of poster abstracts: July 15th E-mail: mssc@unito.it Telephone:+39 011 670 7561 Fax:+39 011 670 7855 Postal address: MSSC2002 Dipartimento di Chimica IFM Via Giuria, 5 I-10125 Torino, Italy From chemistry-request@server.ccl.net Mon Jan 21 12:07:02 2002 Received: from indyf.chem.warwick.ac.uk ([137.205.209.72]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0LH71I27307 for ; Mon, 21 Jan 2002 12:07:01 -0500 Received: (from matt@localhost) by indyf.chem.warwick.ac.uk (SGI-8.9.3/8.9.3) id QAA16817 for chemistry@ccl.net; Mon, 21 Jan 2002 16:58:53 GMT Date: Mon, 21 Jan 2002 16:58:53 +0000 From: MGMS Webmaster To: chemistry@ccl.net Subject: MGMS Press Release Message-ID: <20020121165852.Q14513@indyf.chem.warwick.ac.uk> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i The following press release may be of interest to the CCL. Press Release Molecular Graphics and Modelling Society (MGMS) and Royal Society of Chemistry Molecular Modelling Group (RSC MMG) Encourage Young Researchers! In order to encourage young scientists at the beginning of their careers, the MGMS organises an annual "Young Modellers' Forum" in which postgraduate students present their work on any aspect of computational chemistry or computational biology in front of a learned audience of academic and industrial researchers. This year the meeting took place on November 30th 2001 and was run in conjunction with the Royal Society of Chemistry's Molecular Modelling Group (RSC MMG) and was sponsored by 15 pharmaceutical and software companies (http://www.mgms.org/young2001.htm). The first prize was awarded to Samantha Hughes of the Department of Chemistry at Imperial College, who outlined her research on the asymmetry of a key bacterial enzyme demonstrating that the molecular modelling findings were in good agreement with experimental measurements. The poster prize for 2001 was awarded to Daniele Bemporad of the University of Southampton for his work on the simulation of drugs passing through membranes. Presenting the awards, Dr. David Manallack (the organiser of the meeting and a researcher at Celltech) praised the standard of the presentations: "This year has been outstanding. I've had researchers of 25 years standing telling me they couldn't give presentations as good as the ones we saw today." The Molecular Graphics and Modelling Society is a charitable organisation that promotes and advances public education in the science of molecular graphics and related subjects. Dr. Catherine Burt (of Pfizer Global Research and Development and Chairperson of the Society) expressed the importance of mentoring young scientists. "I am committed to making sure that the society fulfils the essential role of nurturing up-and-coming talent by running poster competitions for students at our meetings and organising a Young Modeller's forum, which helps industry to recruit new people." For further information, please visit the society's web site: http://www.mgms.org -- email: webmaster@mgms.org From chemistry-request@server.ccl.net Mon Jan 21 15:57:14 2002 Received: from schrodinger.com ([192.156.98.99]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0LKvEI32694 for ; Mon, 21 Jan 2002 15:57:14 -0500 Received: from schrodinger.com (amaris.schrodinger.com [192.156.98.121]) by schrodinger.com (8.8.5/8.8.5) with ESMTP id MAA19661; Mon, 21 Jan 2002 12:56:40 -0800 Message-ID: <3C4C8211.82140730@schrodinger.com> Date: Mon, 21 Jan 2002 13:03:13 -0800 From: George Vacek Organization: Schrodinger, Inc. X-Mailer: Mozilla 4.75 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: Pierre Mignon CC: chemistry@ccl.net Subject: Re: CCL:FF, and QM/MM Software References: <3C4C3E63.6080405@vub.ac.be> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Pierre Mignon wrote: > I am interested to buy a software to do QM/MM calcculations and FF > minimalisations for a project concerning biochemistry. Could anybody give me > suggestions and critics upon their use and also on other software ? Pierre, QSite is a mixed Quantum Mechanics/Molecular Mechanics package specially tuned for studying reactive chemistry in biological systems. QSite enables highly accurate studies of protein-ligand interactions including hydrogen-bonding, proton-transfer, charge-transfer reactions, metal-ligand binding and metalloenzyme catalysis. In QSite, the molecular mechanics calculations are performed using the OPLS-AA force field, generally acknowledged to be the most reliable for treating medicinally relevant compounds and proteins. For the QM, QSite benefits from all of Jaguar's strengths, including Jaguar's unique initial guess algorithm that ensures convergence to the correct electronic ground state for metal-containing systems. QSite is able to perform full geometry optimizations and incorporate solvation effects using continuum dielectric methods. More complete information on QSite can be found at http://www.schrodinger.com Regards, George Vacek =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- vacek@schrodinger.com (503) 299-1150 http://www.schrodinger.com/ Schrodinger, Inc., 1500 SW First Ave., Suite 1180, Portland, OR 97201 Every culture that has lost myth has lost, by the same token, its natural, healthy creativity. -- Friedrich Nietzsche "The Birth of Tragedy" 1872 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From chemistry-request@server.ccl.net Mon Jan 21 20:44:58 2002 Received: from postal.sdsc.edu (IDENT:BzchwVyOpBzW3YH2oZvA6+7eRUG3awTx@[132.249.20.114]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0M1iwI09838 for ; Mon, 21 Jan 2002 20:44:58 -0500 Received: from koa.sdsc.edu (IDENT:ua8OZTcO+J46HmuQO/9gX7aJmp0ThMDz@koa.sdsc.edu [132.249.23.116]) by postal.sdsc.edu (8.11.6/8.11.6/SDSCserver/21) with ESMTP id g0M1ifN07686; Mon, 21 Jan 2002 17:44:41 -0800 (PST) Received: from localhost by koa.sdsc.edu (SGI-8.9.3/1.11-IRIXclient) with ESMTP id RAA13110; Mon, 21 Jan 2002 17:44:40 -0800 (PST) Date: Mon, 21 Jan 2002 17:44:40 -0800 From: Wibke Sudholt To: Julien MICHEL cc: Subject: Re: CCL:Hartree fock energy evaluation modus operandi In-Reply-To: <001c01c1a1d9$6946b020$d80ec3d4@sungam> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, perhaps take a look into Szabo/Ostlund, "Modern Quantum Chemistry", Dover, 1996. In Chapter 3.5, details on "Model Calculations on H2 and HeH+" with HF/STO-3G are given. I hope that helps a bit, Wibke Sudholt University of California, San Diego On Sun, 20 Jan 2002, Julien MICHEL wrote: > Dear CCLers, > > I know my request might seem a bit strange, but I'm looking for a document > which would summarize ALL the calculations performed to evaluate the energy > of a simple molecular system using an Hartree-Fock hamiltonien. > Since I'm aware that the computations can become pretty quickly untraceable > I'd like to see a documents which used a simple basis set ( i.e STO-3G ) for > a very simple molecular system (H2 would be the ideal case). > The purpose of this request is to obtain sources to help me perform an > energy evaluation "by-hand". This probably sounds strange as my home > computer would probably be a zillion times faster than I, but altough I'm > aware of the way the self-consistent field theory works, I feel frustrated > to not know exactly what my computer is doing when I perform an Hartree Fock > calculation. > > MICHEL Julien > Graduate student in chemistry > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Mon Jan 21 13:11:20 2002 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0LIBKI28588 for ; Mon, 21 Jan 2002 13:11:20 -0500 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id NAA10044; Mon, 21 Jan 2002 13:11:05 -0500 (EST) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Mon, 21 Jan 2002 13:11:59 -0500 (Eastern Standard Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GQA00IDLVLFUH@lvlmail.unitedcatalysts.com> for chemistry@ccl.net; Mon, 21 Jan 2002 13:05:39 -0500 (EST) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Mon, 21 Jan 2002 13:09:41 -0500 Content-return: allowed Date: Mon, 21 Jan 2002 13:09:38 -0500 From: "Shobe, Dave" Subject: question of netiquette To: "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629D01C158A4@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g0LIBKI28589 Gary Breton wrote: > I had many requests for a summary of the answers. I provide these below > without the names of those responding (which I guess is good etiquette, > could be wrong). I have uncertainties about that myself. There is the arguement that people should get credit for their work/ideas, and there is the argument that privacy should be respected when the response comes from "person to person" e-mail. The usual practice on CCL seems to be to include the names, but I'm not sure that's really the correct thing to do. Any further comments? --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Don't bother flaming me: I'm behind a firewall. From chemistry-request@server.ccl.net Mon Jan 21 22:11:41 2002 Received: from cheetah.it.wsu.edu (root@[134.121.1.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g0M3BfI12987 for ; Mon, 21 Jan 2002 22:11:41 -0500 Received: from enigma (ucis.chem.wsu.edu [134.121.41.180]) by cheetah.it.wsu.edu (8.12.1/8.12.1) with ESMTP id g0M3BKAC010195; Mon, 21 Jan 2002 19:11:20 -0800 (PST) From: "Phillip Matz" To: "'Shobe, Dave'" , "'CCL'" Subject: RE: question of netiquette Date: Mon, 21 Jan 2002 19:11:20 -0800 Message-ID: <000001c1a2f2$772f79f0$1200a8c0@chem.wsu.edu> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.3416 In-Reply-To: <157A51F55AAAD3119CD70008C7B1629D01C158A4@lvlxch01.unitedcatalysts.com> Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-Virus-Scanned: by amavisd-milter (http://amavis.org/) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g0M3BfI12988 How about the following: 1) If the original CCL poster explicitly states they will post summaries then the replier (sp) will take it upon themselves to let the poster know if it is NOT ok to include their name in the posted summary (default assumption is to give credit to all posters; i.e. the burden of desiring and receiving privacy is then up to the person offering their idea) 2) If the original CCL poster does not state they will be posting a summary then the replier should post to the CCL directly (in which case they will receive "idea ownership"), but in the event that the replier communicates with the original poster via private email then the replier must indicate they desire idea ownership (i.e. the default assumption is the replier desires privacy) in the event the original poster is requested to post a summary. Yes? No? Suggestions? Regards, Phil Matz -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net] On Behalf Of Shobe, Dave Sent: Monday, January 21, 2002 10:10 AM To: 'CCL' Subject: CCL:question of netiquette Gary Breton wrote: > I had many requests for a summary of the answers. I provide these > below without the names of those responding (which I guess is good > etiquette, could be wrong). I have uncertainties about that myself. There is the arguement that people should get credit for their work/ideas, and there is the argument that privacy should be respected when the response comes from "person to person" e-mail. The usual practice on CCL seems to be to include the names, but I'm not sure that's really the correct thing to do. Any further comments? --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Don't bother flaming me: I'm behind a firewall. -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net