From owner-chemistry@ccl.net Fri Oct 6 07:23:05 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id HAA13581; Fri, 6 Oct 1995 07:10:18 -0400 Received: from utsc.s.u-tokyo.ac.jp for smori@chem.s.u-tokyo.ac.jp by bedrock.ccl.net (8.6.10/950822.1) id HAA01968; Fri, 6 Oct 1995 07:10:13 -0400 Received: from [133.11.6.102] (nakaquadra.chem.s.u-tokyo.ac.jp) by utsc.s.u-tokyo.ac.jp (5.67+1.6W/TISN-1.3/R2) id AA03256; Fri, 6 Oct 95 20:05:08 JST Message-Id: <9510061105.AA03256@utsc.s.u-tokyo.ac.jp> Date: Fri, 6 Oct 1995 20:08:57 +0900 To: chemistry@ccl.net From: smori@chem.s.u-tokyo.ac.jp (Mori Seiji) X-Sender: smori@chem.s.u-tokyo.ac.jp (Unverified) Subject: AIMPAC PROGRAM Cc: smori@utsc.s.u-tokyo.ac.jp Mime-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) Dear Netters, I would like to get AIMPAC series programs which R. W. F. Bader,et al developped and which contains the calculation of the Laplacian of charge density. Ref. is J. Comput. Chem, 3, 317 (1982) , however, there is no journal in my university. How should I get this programs and manuals? Points of question: (1) How to contact? (2) Free or not? If I need costs, how much? (3) I use IBM RISC/6000 (AIX 3.2.5). Could I use it in this workstation? SIncerely yours, smori ============================(^-^)=========================== Seiji Mori Nakamura Lab. Department of Chemistry The University of Tokyo Tel: 03-3812-2111 ext.4647 FAX: 03-5800-6889 Address: 7-3-1, Hongou, Bunkyo-ku, Tokyo 113, JAPAN email: smori@chem.s.u-tokyo.ac.jp From owner-chemistry@ccl.net Fri Oct 6 08:38:06 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id IAA14534; Fri, 6 Oct 1995 08:34:19 -0400 Received: from csb0.IPC.PKU.EDU.CN for zhy@csb0.IPC.PKU.EDU.CN by bedrock.ccl.net (8.6.10/950822.1) id IAA02363; Fri, 6 Oct 1995 08:34:10 -0400 Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@ccl.net id AA17401; Fri, 6 Oct 95 20:10:05 -0700 Date: Fri, 6 Oct 1995 20:10:04 -0700 (PDT) From: Zhang Hongyu To: COMP_CHEM_LIST Cc: "FOUNTAIN, KEN" Subject: Summary: clustering according to internal coordinates, Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL'ers, Two weeks ago, I posted a question on clustering according to internal coordinates, although there's no many responses, I'd still like to give a summary. BTW, I am sorry for an address error in last post, this time it is definately right. More infomation is welcome, especially for free code. Henry ---------------------------------------------------------------------- Henry Hongyu Zhang, Ph.D. student | email: zhy@ipc.pku.edu.cn Molecular Design Laboratory | zhy@pschnetware.pku.edu.cn Institute of Physical Chemistry | Tel: 8610-2501490 Peking University | Fax: 8610-2501725 Peking 100871 , China | URL: http://www.ipc.pku.edu.cn/moldsgn/ | zhy/hom.htm ----------- Too hard, to be broken Too soft, to be worthless ------------ Old Chinese Saying ======================================================================== My original post, > I've got from a simulated annealing process a group of conformations of a > penta-ptide with 3D coordinates, and want to cluster them according to > internal coordinates, i.e. value of Phi and Psi angle, but I haven't found > the relative function in SYBYL or QUANTA. Can anyone tell me where to find > suitable softwares ? > > BTW, I also want to get the standard of dividing Ramanchandra graph > (explicit value), i.e., if I got a pair of Phi-Psi value, how can I tell > whether it fall into A,D,or D*? -------- From: shenkin@still3.chem.columbia.edu (Peter Shenkin) Our program, XCluster, is designed to do exactly this. It's included with MacroModel, which isn't free, but is very cheap to academics. For further info, "finger mmod@still3.chem.columbia.edu". If you visit our WWW home page and work your way down to a description of the XCluster program, you'll see some images that show what clusters of conformations look like if the ensemble indeed exhbits strong clustering. Our home page is: http://www.cc.columbia.edu/~chempub/mmod/mmod.html XCluster can work in either torsional space or in Cartesian space; the user decides at run-time. You can read more about XCluster in: Shenkin & McDonald, J. Comput. Chem., v.15, pp.899-916, 1994. Also, the latest version of MacroModel, Version 5.0, includes converters that translate from SYBYL Mol2 format to MacroModel format (and vice versa) -- so if you've been using SYBYL, it ought to be easy to get your conformations into a format that MacroModel can understand. > BTW, I also want to get the standard of dividing Ramanchandra graph > (explicit value), i.e., if I got a pair of Phi-Psi value, how can I tell > whether it fall into A,D,or D*? XCluster doesn't do this for you; sorry. But the way I'd do this is to print out the Phi-Psi values (MacroModel can do this for you). Then calculate the distance of each pair to the "generic" pair value for the A, D and D* regions, taking the periodicity of angle space into account. The "generic" pair value a given Phi-Psi pair is closest to defines which region it belongs to. -P. ******** When somebody says, "It's a matter of principle,"... ******** *Peter S. Shenkin, Box 768 Havemeyer Hall, Chemistry, Columbia Univ.,* *NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039* ************ ...it's a sure sign he wants the whole pie. ************* ------------ From h0159cap@rz.hu-berlin.de Fri Sep 15 15:25:19 1995 Dear Henry, > I've got from a simulated annealing process a group of conformations of a > penta-ptide with 3D coordinates, and want to cluster them according to > internal coordinates, i.e. value of Phi and Psi angle, but I haven't found > the relative function in SYBYL or QUANTA. Can anyone tell me where to find > suitable softwares ? Along with software, it might be useful to inspekt a certain selection of conformers by eye ! Often, the best is to first cluster on hydrogen bonding (using any criteria for HB), and then look at only backbone dihedrals to subdivide groups with same hydrogen bonds. > BTW, I also want to get the standard of dividing Ramanchandra graph > (explicit value), i.e., if I got a pair of Phi-Psi value, how can I tell > whether it fall into A,D,or D*? You should find this in Zimmerman, S.S. & Scheraga, H.A. Biopolymers 1977, v. 16, 811-843. Regards, Frank Eisenmenger +------------------------------------------------------------------------+ | Institute of Biochemistry | | Medical Faculty of the Humboldt University (Charite) | | | | Hessische Str. 3-4 | | 10115 Berlin, Germany | | | | Phone: +49-30-28468-612 or -239 FAX: +49-30-28468-600 | | E-mail: eisenmenger@rz.hu-berlin.de | +------------------------------------------------------------------------+ ------ From: "FOUNTAIN, KEN" Hi Henry, I'd be very interested in whatever you find out about this. Could you please post to the list any answers you get. BTW, my son, Daniel Fountain, is at Peking Language university in the Friendship Dormatory. If you get over that way please look him up and introduce yourself. He is a graduated chemical engineer >from Georgia Tech, who is studying Chinese language and culture for two years in your country. I'm sure he would like to see someone who is talking to his father. Sincerely, Ken Fountain Professor of Chemistry Truman/Northeast Miussouri State University ---------------- From: Mrigank To: chemistry@www.ccl.net I have written a program which can find phi, psi, omega and chis from PDB or MoMoS format files and output in a cpmpact tabular or a GNUPLOT script that also markout the Ramachandran allowed regions. It is in Fortran. If interested i can send it . Mrigank ---- /Mrigank \/ Phone +91 172 690557 \ \Institute of Microbial Technology /\ FAX: +91 172 690585 / /Sector 39A, \/ Email: mrigank@imtech.ernet.in \ \Chandigarh 160 014 India. /\ mrigank@csimtech.ren.nic.in / \//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\// Science does not have a country, But Scientist has one -L. Pastuer From owner-chemistry@ccl.net Fri Oct 6 11:23:11 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id LAA18398; Fri, 6 Oct 1995 11:13:08 -0400 Received: from faui45.informatik.uni-erlangen.de for jmolmod@organik.uni-erlangen.de by bedrock.ccl.net (8.6.10/950822.1) id LAA03917; Fri, 6 Oct 1995 11:12:52 -0400 Received: from derioc1.organik.uni-erlangen.de (derioc1.organik.uni-erlangen.de [131.188.128.1]) by uni-erlangen.de with ESMTP id QAA21093 (8.6.12/7.4f-FAU); for ; Fri, 6 Oct 1995 16:12:21 +0100 Received: (from jmolmod@localhost) by organik.uni-erlangen.de id QAA12467 (8.6.12/7.4f-FAU); for chemistry@ccl.net; Fri, 6 Oct 1995 16:04:52 +0100 From: Journal of Molecular Modeling Message-Id: <199510061504.QAA12467@derioc1.organik.uni-erlangen.de> Subject: Acceptance of the J.Mol.Model. WWW-homepage To: chemistry@ccl.net Date: Fri, 6 Oct 95 16:04:39 MET X-Mailer: ELM [version 2.3 PL11] THANKS ! The Journal of Molecular Modeling has gained a very wide acceptance. We did count a total of 150,000 visits to the Journal of Molecular Modeling WWW-homepage in the first 39 weeks of operation and a peak of almost 12,500 visits in one week. We are currently running at a steady 8,000 visits per week, which suggests that people are using the Journal of Molecular Modeling abstracts actively. Once again, thanks for your support. Best wishes Tim Clark If you have a good paper looking for a home - don't forget us. ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^ Journal of Molecular Modeling ^ Tel: [+49](0)9131 / 85-2948 ^ ^ Computer-Chemie-Centrum ^ [+49](0)9131 / 85-6567 ^ ^ Universitaet Erlangen-Nuernberg ^ ^ ^ Naegelsbachstrasse 25 ^ Fax: [+49](0)9131 / 85-6565 ^ ^ D-91052 Erlangen ^ ^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^ email: jmolmod@organik.uni-erlangen.de ^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^ URL: http://www.organik.uni-erlangen.de/info/JMOLMOD/jmolinfo.html ^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ From JSMCM@jazz.ucc.uno.edu Fri Oct 6 13:38:14 1995 Received: from jazz.ucc.uno.edu for JSMCM@jazz.ucc.uno.edu by www.ccl.net (8.6.10/950822.1) id NAA20642; Fri, 6 Oct 1995 13:24:03 -0400 Received: from jazz.ucc.uno.edu by jazz.ucc.uno.edu (PMDF #2820 ) id <01HW4BNW45DG92GLJ7@jazz.ucc.uno.edu>; Fri, 6 Oct 1995 12:23:12 CST Date: 06 Oct 1995 12:23:12 -0600 (CST) From: "Dr. Jorge Seminario" Subject: Absolute binding free energy To: CHEMISTRY@www.ccl.net Cc: bruce_bush@merck.com Message-id: <01HW4BNW45DI92GLJ7@jazz.ucc.uno.edu> X-VMS-To: IN%"CHEMISTRY@www.ccl.net" X-VMS-Cc: IN%"bruce_bush@merck.com",JSMCM MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear CCL's: I am posting the following query from a subscriber of the "water-list" who is not in the CCL. Please, if you answer to the list also send a copy to his address. Regards Jorge Seminario ================================================================= From: bruce_bush@merck.com Calculated "Absolute" binding free energies: what are they? I posed this question to the Water Science Network on 15 Sept 95. I have a tentative answer, based on further thought and sharpened by useful responses (thanks to Drs. Berendsen, Cramer, Stouton). Comments welcome. What do computationalists mean when they report the "ABSOLUTE free energy of binding" and compare this with a simulation energy? Example: J. Aqvist et al, Protein Engineering 7(3), 385-391 (1994); also papers by Kollman, Hermans, Warshel, etc. These calculations are always based on averages of some sort, in which no volume or density appears explicitly. But "absolute" free energy of binding should correspond somehow to a dissociation constant which has units of CONCENTRATION: [A(free)][R(free)] / [A:R(bound)] Taking logarithm ln() of Kd requires us to choose some arbitrary unit of concentration. (Molar, 1 M, is based on radius of earth and density of water. Nanomolar, 1 nM, is based on these quantities plus # of fingers on 2 hands.) Free energy of TRANSFER between two homogeneous media (solvents or gas phase) corresponds to a ratio of concentrations. RELATIVE binding free energy is also a ratio of concentrations (Kd's). Neither one raises any difficulty in princple. The simulation yields an average energy which gives this ratio: delta-G = -kT ln (c2/c1). How can a free-energy calculation "build in" the units of concentration when calculating 'absolute' binding free energy, but not contain any unit of concentration when calculating relative free energies? Tentative answer: a) Most computational papers dealing with 'absolute' binding free energy don't address this question. The simulation reports an average energy; the authors workers either do or do not adjust this energy. Then they compare the result with experimental dissociation constants in units 1M. b) There's no problem in principle when simulating free energy of transfer. by "turning on" interactions of A with the homogeneous solvent. Any assumption of standard concentration or volume affects both the interacting and the noninteracting state equally, and cancels out of the final result. The same holds for transfer between solvents. c) There's no problem when simulating relative binding free energy (B:R-A:R) because it involves 'growing' A to B in the context of the receptor R and also 'growing' A to B in homogeneous solvent. The simulation within the receptor is insensitive to the size of the box; and as before, the simulation within homogeneous fluid can also be made independent of box size. [Remarks (b) and (c) but apply also to 'particle insertion' or 'thermodynamic perturbation' or any other AVERAGING method.] d) Simulations of absolute binding free energy are subtly different from either absolute TRANSFER free energy or RELATIVE binding free energy. They involve growing "null" to "A" to "B" in the context of the receptor. Workers treat this formally as the same as growing "A" to "B". But at the very endpoint of the simulation, as ligand "A" becomes "null" or is created from "null", the ligand gains (or loses) the ability to wander through all of the simulation volume. If the simulation is done carefully enough, this last stage is a hugely expensive estimate of the the ratio of volumes of simulation 'box' to the binding site. The logarithm of this ratio is an entropic free energy. Thus, => e) the implicit 'standard state' of an absolute binding free energy simula- tion is (1 ligand per simulation box), if the end point is sampled well. f) The state "1M" happens correspond to 1 ligand in a box of side 12A. Even if workers forget to adjust for the size of the simulation 'box' (typically about 30A on a side) the result, compared to Kd in molar, appears sensible within an order of magnitude, and doesn't raise any 'flags'. I haven't seen this argument spelled out, though Ben-Naim's careful discussions of 'cratic' and 'unitary' entropy certainly address the same issues in the context of transfer free energies. Your comments are welcome. / Bruce/ bruce_bush@merck.com Merck Research Labs, Rahway NJ 07065 ================================================================= From owner-chemistry@ccl.net Fri Oct 6 13:53:10 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id NAA21063; Fri, 6 Oct 1995 13:42:04 -0400 Received: from rani.chem.yale.edu for lim@rani.chem.yale.edu by bedrock.ccl.net (8.6.10/950822.1) id NAA05585; Fri, 6 Oct 1995 13:41:53 -0400 Received: by rani.chem.yale.edu; Fri, 6 Oct 95 13:41:28 -0400 From: Dongchul Lim Message-Id: <9510061741.AA21686@rani.chem.yale.edu> Subject: DFT frequency scaling factor To: chemistry@ccl.net (Computational Chemistry) Date: Fri, 6 Oct 95 13:41:27 EDT X-Mailer: ELM [version 2.3 PL11] I'd like to thank those who replied to my question regarding DFT frequency scaling factors. -Dongchul Lim, lim@rani.chem.yale.edu >Are there scaling factors for frequencies from different >DFT methods, especially BECKE3LYP? -------------------------------------------------------------------- The scaling factor for BECKE3LYP seems pretty close to one, 0.989 according to one study, see: C. W. Bauschlicher and H. Partridge, J. Chem. Phys. 98 (1994) 11623. I think that even for non-empirical functionals (LDA, Perdew's GGA) scaling factors would not help much (they would probably turn out close to one). |-------------------------------|-----------------------------| | Rene Fournier | fournier@physics.unlv.edu | | Department of Physics | fournie@ned1.sims.nrc.ca | | University of Nevada | phone : (702) 895 1706 | | Las Vegas, NV 89154-4002 USA | FAX : (702) 895 0804 | |-------------------------------|-----------------------------| -------------------------------------------------------------------- For the B-LYP method, the scaling factor is close to one. However, a scale factor of 0.9613 is required for the Becke3LYP method for reliable prediction of fundamental frequencies. The 0.9613 value was derived from comparison with experimental frequencies of a large set of molecules (1066 frequencies for 122 molecules). ++~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~++ || __ |\ Dr. Ming Wah (Richard) Wong || || / |_| \ -----------------------------------------------|| || .' \ Department of Chemistry || || / *\ The University of Queensland || || \ __ / Brisbane, Qld 4072, Australia || || \_.-' \_ / Fax: +61 7 3365 4299 | Phone: +61 7 3365 3829 || || v email address: wong@chem.chemistry.uq.oz.au || ++~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~++ -------------------------------------------------------------------- >From AZHARI@FRCU.EUN.EG Thu Oct 5 07:42:14 1995 Look at the 24 of August issue of JPC. I do not remember the exact page number but the title of the paper is Correlated ab initio force fields and vibrational analysis for ioxaozle and isothiazole by Adel A. El-Azhary and Hans U. Suter. Adel El-Azhary -------------------------------------------------------------------- >From aps501@anugpo.anu.edu.au Wed Oct 4 18:45:31 1995 WE are currently finalizing the writeup of just such a study. If you would like to know the scaling factors for a variety of DFT methods drop me a line. In the meantime I can point you to a recent paper by Pulay (JPC, 1995, 99, 3093) Kind Regards, Anthony P. Scott From elewars@alchemy.chem.utoronto.ca Fri Oct 6 14:23:11 1995 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.6.10/950822.1) id OAA22034; Fri, 6 Oct 1995 14:09:36 -0400 Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.6.10/8.6.10) id OAA13539 for chemistry@www.ccl.net; Fri, 6 Oct 1995 14:09:33 -0400 Date: Fri, 6 Oct 1995 14:09:33 -0400 From: "E. Lewars" Message-Id: <199510061809.OAA13539@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: AIMPAC Re geyying AIMPAS: Contact research group of Prof Richard Bader bader@mcmail.cis.mcmaster.ca OR bade@ccsvax.cis.mmaster.ca OR bader@babbage.chemistry.McMaster.CA Errol Lewars ==== From stoutepf@chemsci5.dmpc.com Fri Oct 6 15:38:12 1995 Received: from gatekeeper.es.dupont.com for stoutepf@chemsci5.dmpc.com by www.ccl.net (8.6.10/950822.1) id PAA24424; Fri, 6 Oct 1995 15:36:36 -0400 Received: by gatekeeper.es.dupont.com; id AA15673; Fri, 6 Oct 95 15:36:29 -0400 Received: from [158.117.200.143] (llm200143.dmpc.com) by chemsci5.dmpc.com (5.0/SMI-SVR4) id AA13733; Fri, 6 Oct 1995 15:34:46 -0400 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Organization: The DuPont Merck Pharmaceutical Company X-Mailer: Eudora Pro 2.1.3 for Macintosh X-Url: http://www.halcyon.com/stouten/index.html Date: Fri, 6 Oct 1995 15:32:25 -0400 To: CHEMISTRY@www.ccl.net From: stoutepf@chemsci5.dmpc.com (Pieter Stouten) Subject: Re: CCL:Absolute binding free energy Cc: JSMCM@jazz.ucc.uno.edu Content-Length: 2814 At 12:23 95/10/06, Dr. Jorge Seminario wrote: >Dear CCL's: I am posting the following query from a >subscriber of the "water-list" who is not in the CCL. I already sent the following to Bruce Bush (bruce_bush@merck.com) after his request appeared on the Water Science Network (WSN, a *very* interesting list; subscribe by sending mail to listserv@gibbs.oit.unc.edu, with the command "subscribe water " in the body). If there is any interest, I can forward to CCL the other WSN responses to Bruce's query (I did not keep them all, though). Cheers, Pieter. --------------------------------------------------------------------------- << start of forwarded material >> | |Date: Wed, 20 Sep 1995 12:33:27 -0400 |To: bruce-bush@merck.com |From: stoutepf@chemsci5.dmpc.com (Pieter Stouten) |Subject: Re: WSN: "Absolute" binding energies: what are they? | |Hi Bruce, | |There are no assumptions in the relationship between Ki and binding free |energy. It's all a matter of definitions, specifically the definition of |G(0) or more correctly mu(0). | |In dilute solutions, the thermodynamic potential of compound i is defined |as | | mu(i) = mu(i,0) + RT ln A(i)/A(i,0) | |where mu(i,0) is the thermodynamic potential under standard conditions and |A(i)/A(i,0) is the activity with respect to the standard conditions. Since |standard conditions for a compound in solution are defined as A(i,0) = 1 |mol/l (or 1 mol/kg), one should express A(i) in mol/l to obtain a |dimensionless quantity. If standard conditions were defined otherwise, |mu(i,0) would change, but RT ln A(i)/A(i,0) would exactly compensate that |so that mu(i) stays the same. | |The binding free energy for a ligand L to receptor R is | | delta G(R+L -> RL) = mu(RL) - mu(R) - mu(L) | |With A(i,0) = 1 mol/l for all compounds, this becomes | | delta G(R+L -> RL) = mu(RL,0) - mu(R,0) - mu (L,0) + RT ln A(RL) - | RT ln A(R) - RT ln A(L) | = delta G(R+L -> RL,0) + RT ln A(RL)/(A(R)*A(L)) | |Since delta G(R+L -> RL) = 0 (equilibrium), | | delta G(R+L -> RL,0) = - RT ln A(RL)/(A(R)*A(L)) | |or | delta G(R+L -> RL,0) = RT ln Kd | |Note that what is generally referred to as the binding free energy is |actually delta G(R+L -> RL,0), the binding free energy *under standard |conditions*. | |Hope this helps. | |Cheers, Pieter. | |-- | |Pieter Stouten || Nothing shocks me; |Computer Aided Drug Design Group || |The DuPont Merck Pharmaceutical Company || I am a scientist! |P.O. Box 80353, Wilmington, DE 19880-0353 || |Phone: +1 (302) 695 3515 || -- |Fax: +1 (302) 695 2813 || |Internet: stoutepf@chemsci5.dmpc.com || Indiana Jones | << end of forwarded material >> From chpajt@bath.ac.uk Fri Oct 6 15:53:12 1995 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by www.ccl.net (8.6.10/950822.1) id PAA24611; Fri, 6 Oct 1995 15:43:52 -0400 Received: from bath.ac.uk (actually host mary.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Fri, 6 Oct 1995 20:43:44 +0100 Date: Fri, 6 Oct 1995 20:43:37 +0100 (BST) From: A J Turner To: CHEMISTRY@www.ccl.net Subject: Re: Charmm vanishing atoms In-Reply-To: <9510050636.AA10113@parcom.parcom.ernet.in> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! Just one more thing - I noticed that the minimisation stage gave no proximity warings whilst the dynamics gave lots of warnings for close atoms - is this a symptom? Cheers Alex +--------------------------------------------------+ |Alternate E-mail A.J.Turner@Bath.ac.uk | |www home @ http://www.bath.ac.uk/~chpajt/home.html| +--------------------------------------------------+ From chpajt@bath.ac.uk Fri Oct 6 15:54:16 1995 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by www.ccl.net (8.6.10/950822.1) id PAA24552; Fri, 6 Oct 1995 15:41:30 -0400 Received: from bath.ac.uk (actually host mary.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Fri, 6 Oct 1995 20:31:22 +0100 Date: Fri, 6 Oct 1995 20:31:05 +0100 (BST) From: A J Turner To: chemistry@www.ccl.net Subject: Re: Vanishing atoms in Charmm dynamics In-Reply-To: <199510061809.OAA13539@alchemy.chem.utoronto.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all. I must thank you all for the help that you have supplied so far. I have a very strange one for you now. I have a quenched dynamics run going on Charmm 22.2, using 15A TIP3 sphere to dissolve methyl- glycoside. I used ABNR to minimise to tolgrd 0.001 and then used a fairly standard quenched dynamics run. The snag is that after 300 steps then program says that some of the atoms have undefined co-ordinates. Has anyone every come across this before. Can anyone help. Thanks in advance Alex +--------------------------------------------------+ |Alternate E-mail A.J.Turner@Bath.ac.uk | |www home @ http://www.bath.ac.uk/~chpajt/home.html| +--------------------------------------------------+ From owner-chemistry@ccl.net Fri Oct 6 16:38:13 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id QAA25375; Fri, 6 Oct 1995 16:29:09 -0400 Received: from Princeton.EDU for jimreho@phoenix.Princeton.EDU by bedrock.ccl.net (8.6.10/950822.1) id QAA07572; Fri, 6 Oct 1995 16:29:05 -0400 Received: from ponyexpress.Princeton.EDU by Princeton.EDU (5.65b/2.122/princeton) id AA02148; Fri, 6 Oct 95 11:58:40 -0400 Received: from phoenix.Princeton.EDU (phoenix.Princeton.EDU [128.112.128.43]) by ponyexpress.Princeton.EDU (8.6.12/8.6.12) with ESMTP id LAA19942 for ; Fri, 6 Oct 1995 11:58:37 -0400 Received: (jimreho@localhost) by phoenix.Princeton.EDU (8.6.12/8.6.12) id LAA07578 for chemistry@ccl.net; Fri, 6 Oct 1995 11:58:28 -0400 Message-Id: <199510061558.LAA07578@phoenix.Princeton.EDU> From: jimreho@phoenix.Princeton.EDU (James H. Reho) Date: Fri, 6 Oct 1995 11:58:28 EDT X-Mailer: Mail User's Shell (7.2.2 3/2/90) To: chemistry@ccl.net Subject: Triplet dimers Hello! I am a user of Gaussian 92. Currently I am trying to reproduce calculations for the HF of the triplet Li2 ground state. This state should be totally repulsive; however, using the 6-311G** basis set and SCANning R, I experi ence a rise in energy far too early. This rise then decreases, and the expected exponential increase as R shrinks occurs. I am afraid to trust my calculation as long as this is occurring. Any ideas?? I would greatly appreciate any help. Thanks, jimreho@phoenix.princeton.edu From owner-chemistry@ccl.net Fri Oct 6 20:38:16 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id UAA29186; Fri, 6 Oct 1995 20:28:31 -0400 Received: from utsc.s.u-tokyo.ac.jp for smori@chem.s.u-tokyo.ac.jp by bedrock.ccl.net (8.6.10/950822.1) id UAA09117; Fri, 6 Oct 1995 20:28:28 -0400 Received: from [133.11.6.102] (nakaquadra.chem.s.u-tokyo.ac.jp) by utsc.s.u-tokyo.ac.jp (5.67+1.6W/TISN-1.3/R2) id AA06452; Sat, 7 Oct 95 09:23:24 JST Message-Id: <9510070023.AA06452@utsc.s.u-tokyo.ac.jp> Date: Sat, 7 Oct 1995 09:27:14 +0900 To: chemistry@ccl.net From: smori@chem.s.u-tokyo.ac.jp (Mori Seiji) X-Sender: smori@chem.s.u-tokyo.ac.jp (Unverified) Subject: Thank you for your replys about AIMPAC Mime-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) Dear Drs. E. Lewars, P. Bultinck, K. E. Laidig and Mr. T. Senju. Thank you for your replys in my question about the request of Professor Bader's AIMPAC. SIncerely yours, smori ============================(^-^)=========================== Seiji Mori Nakamura Lab. Department of Chemistry The University of Tokyo Tel: 03-3812-2111 ext.4647 FAX: 03-5800-6889 Address: 7-3-1, Hongou, Bunkyo-ku, Tokyo 113, JAPAN email: smori@chem.s.u-tokyo.ac.jp From cis@cheminnovation.com Fri Oct 6 23:53:19 1995 Received: from connectnet1.connectnet.com for cis@cheminnovation.com by www.ccl.net (8.6.10/950822.1) id XAA01206; Fri, 6 Oct 1995 23:51:35 -0400 Received: from henryl.connectnet.com (henryl.connectnet.com [204.252.2.63]) by connectnet1.connectnet.com (8.6.12/CN-CONFIG-0.2) with SMTP id UAA21478 for ; Fri, 6 Oct 1995 20:51:26 -0700 Date: Fri, 6 Oct 1995 20:51:26 -0700 Message-Id: <199510070351.UAA21478@connectnet1.connectnet.com> X-Sender: henryl@connectnet.com X-Mailer: Windows Eudora Version 1.4.4 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: cis@connectnet.com (ChemInnovation Software) Subject: Chemistry 4-D Draw -- NEW SOFTWARE! Dear Colleagues: This is a note to inform you that Chemistry 4-D Draw Professional 2.1 is now available. Chemistry 4-D Draw is a new generation of drawing program which understands chemists' language -- IUPAC nomenclature. It allows you to create high-quality structures simply by entering molecular names. It includes a full set of intelligent tools for drawing, text and structure editing, and labeling. Features include: * Create/Edit structures in 2D, 3D or 4D (Name space) * Import/Export MDL MOL files * Export publication quality graphics using OLE-2 technologies (Drag&Drop) * Save fragments with your own "trivial names" Available on ALL major PC platforms: Windows 95, Windows 3.1, Windows NT, Macintosh, OS/2 For more information, please see http://www.cheminnovation.com or contact ChemInnovation Software at Tel (619)566-2846 Fax (619)566-4138 E-mail: cis@cheminnovation.com Thank you.