From mbu!neel@vigyan.ernet.in Fri Aug 27 07:44:07 1993 Received: from relay2.UU.NET for mbu!neel@vigyan.ernet.in by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA16383; Fri, 27 Aug 1993 01:26:14 -0400 Received: from spool.uu.net (via LOCALHOST) by relay2.UU.NET with SMTP (5.61/UUNET-internet-primary) id AA28247; Fri, 27 Aug 93 01:26:13 -0400 Received: from sangam.UUCP by uucp5.uu.net with UUCP/RMAIL (queueing-rmail) id 012416.29163; Fri, 27 Aug 1993 01:24:16 EDT Received: from vigyan!mbu.UUCP by sangam.ncst.ernet.in (4.1/SMI-4.2-ERNET-relay) with UUCP id AA12221; Fri, 27 Aug 93 10:45:09+0530 From: mbu!neel@vigyan.ernet.in Received: by iisc.ernet.in (ERNET-IISc/AT&T UNIX SYS V.3.2) id AA23277; Fri, 27 Aug 93 11:44:07 EDT Date: Fri, 27 Aug 93 11:44:07 EDT Message-Id: <9308271544.AA23277@iisc.ernet.in> Received: by vigyan.iisc.ernet.in (smail2.3) id AA09431; 27 Aug 93 10:36:57 EST (Fri) To: vigyan!chemistry@ccl.net Subject: qustion regarding molecular dynamics simulation Q. How can integration of Newtons eq. of motion can be justified in the absence of real solvent molecule while simulating a protein or a dna motion motion ? What about friction offered by solvent ? From arne@mango.mef.ki.se Fri Aug 27 13:37:12 1993 Received: from mango.mef.ki.se for arne@mango.mef.ki.se by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA21731; Fri, 27 Aug 1993 07:36:05 -0400 Received: by mango.mef.ki.se (AIX 3.1/UCB 5.61/4.03) id AA05328; Fri, 27 Aug 93 13:37:12 GMT Date: Fri, 27 Aug 93 13:37:12 GMT From: arne@mango.mef.ki.se (Arne Elofsson) Message-Id: <9308271337.AA05328@mango.mef.ki.se> To: CHEMISTRY@ccl.net Subject: RE: MD MD simulation in absence of water .... It has in several studies been shown that To fully exclude water not is very good. I have a paper i J.Mol.Biol (inpress) but there have been several earlier papers also. The main conclusion is (I think most people agree) Do include water, the solvent effect can be reproduced rather well with specific solvent potentials but they seem to be slower than to include specific waters. (Chris Sander had a paper in last J.M.B with something that sounded very fast.) I do not think that it is neccesary to include a large box of water a few layers of water should be enough. An excellent paper is : Guenot & Kollman J. Comp.Chem.14(3) 295-311 your arne From roberto@demilo.boston.sgi.com Fri Aug 27 03:59:10 1993 Received: from sgi.sgi.com (SGI.COM) for roberto@demilo.boston.sgi.com by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA22175; Fri, 27 Aug 1993 07:59:24 -0400 Received: from relay.sgi.com by sgi.sgi.com via SMTP (920330.SGI/910110.SGI) for chemistry@ccl.net id AA10490; Fri, 27 Aug 93 04:59:22 -0700 Received: from sgibos.boston.sgi.com by relay.sgi.com via SMTP (920330.SGI/920502.SGI) for @sgi.sgi.com:chemistry@ccl.net id AA21376; Fri, 27 Aug 93 04:59:19 -0700 Received: from demilo.boston.sgi.com by sgibos.boston.sgi.com via SMTP (920330.SGI/911001.SGI) for @sgi.com:GDURST@elinet1.dowelanco.com id AA18285; Fri, 27 Aug 93 07:59:15 -0400 Received: from localhost.boston.sgi.com by demilo.boston.sgi.com via SMTP (930416.SGI/920502.SGI) for @sgibos.boston.sgi.com:chemistry@ccl.net id AA26411; Fri, 27 Aug 93 07:59:11 -0400 Message-Id: <9308271159.AA26411@demilo.boston.sgi.com> To: "Gregory L. Durst - DowElanco Discovery Research" Cc: chemistry@ccl.net Subject: Re: IRIX 5.0.1 & MOPAC 6.0?? In-Reply-To: Your message of "Thu, 26 Aug 93 12:45:35 EDT." <930826124535.21a2@ELINET1.DOWELANCO.COM> Reply-To: roberto@boston.sgi.com Date: Fri, 27 Aug 93 07:59:10 EDT From: Roberto Gomperts Your message dated: Thu, 26 Aug 93 12:45:35 EDT |> Dear netters, |> |> We recently upgraded one of our SGI servers to an Onyx running IRIX 5.0.1 |> and have seen a problem running MOPAC 6.0 with ESP options compiled in. |> Now when we run a MOPAC job, the machine is unable to execute any |> other programs. Things just won't run! Never seen anything like this before. |> Errors appear in the console window stating things like: |> |> NOTICE: dupreg - temporarily insufficient memory to allocate virtual swap space, |> process buttonfly [1592] |> |> OR |> |> NOTICE: growreg - temporarily insufficient memory to expand region, process |> sybyl [1596] |> |> This does *not* happen on our other SGI server running IRIX 4.0.5. and if |> we use a copy of MOPAC 6.0 without the ESP modules compiled in, there is |> no problem on the new Onyx...I'm now very suspicious that the problem |> has something to do with the new OS and the ESP modules in MOPAC 6.0. |> Anybody seen anything similar? |> Thanks in advance for any help! |> Greg Durst Hi Greg, I am responding to you via the net because the answer will benefit other people seeing the same problem on the new OS for Challenge/Onyx systems. The origin of the problem has to do with new ways of allocating swap space. There is a new feature (for SGI): virtual swap space that will allow you to, on the fly, correct this situation. Become superuser (root) and issue the following sequence of commands: touch /usr/tmp/vswap swap -a -p2 -v2000000 /usr/tmp/vswap Please read the man page of swap to get more info and what to do to ensure that the virtual swap space is there after a reboot. The inappropriate default setting of the machine should be corrected in the next release of the OS. I hope this helps and apologies for the inconvenience. -- Roberto Roberto Gomperts roberto@sgi.com phone: (508) 562 4800 Fax: (508) 562 4755 "Gracias a la vida, que me ha dado tanto ..." Violeta Parra From ravishan@tulip.wcc.wesleyan.edu Fri Aug 27 04:44:20 1993 Received: from tulip.wcc.wesleyan.edu for ravishan@tulip.wcc.wesleyan.edu by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA23624; Fri, 27 Aug 1993 08:45:39 -0400 Received: by tulip.wcc.wesleyan.edu (AIX 3.2/UCB 5.64/4.03) id AA18275; Fri, 27 Aug 1993 08:44:20 -0400 Date: Fri, 27 Aug 1993 08:44:20 -0400 Message-Id: <9308271244.AA18275@tulip.wcc.wesleyan.edu> From: G. Ravishanker Sender: ravishan@tulip.wcc.wesleyan.edu To: mbu!neel@vigyan.ernet.in Cc: chemistry@ccl.net In-Reply-To: <9308271544.AA23277@iisc.ernet.in> (message from swan.wesleyan.edu!vigyan.ernet.in!mbu!neel on Fri, 27 Aug 93 11:44:07 EDT) Subject: Re: qustion regarding molecular dynamics simulation >> Q. How can integration of Newtons eq. of motion can be justified in the >> absence of real solvent molecule while simulating a protein or a dna >> motion motion ? What about friction offered by solvent ? In the absence of solvent, the model you are studying is usually the system "in vacuo". This is usually done to check if any unusual artifacts exist in the force field and used to be the only way one could study systems in the early days, due to the lack of computational resources. This therefore has very limited "physical" significance, such as correlation to experimental data etc. (I am talking about large biomolecular systems here) Solvent can be modelled in several different ways. The extremes being explicit solvents (TIP4P, SPC are some of the examples) and a simple continum model using a constant dielectric in the modulation of electrostatic interaction between the solute atoms. The expense of computation varies according to the model and is pretty obvious. When these models are used to solve Newton's equations of motion using the forces on atoms, it is called Molecular Dynamics. The type of model you are interested in, where you want to model friction of the solvent, you use a different set of equations typically. These are the stochastic Langevin equations, where in addition to the forces, a stochastic term to represent the solute-solvent collisions and a frictional term to express the drag due to solvent appear in the equation. Please refer to an excellent review by W.F. van Gunsteren and H.J.C. Berendsen on all these issues (Angew. Chem. Int. Ed. Engl. v. 29, 992-1023(1990) as well as Allen and Tildesley's book. Ravi From shenkin@still3.chem.columbia.edu Fri Aug 27 04:38:12 1993 Received: from mailhub.cc.columbia.edu for shenkin@still3.chem.columbia.edu by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA23333; Fri, 27 Aug 1993 08:39:41 -0400 Received: from merhaba.cc.columbia.edu by mailhub.cc.columbia.edu with SMTP id AA08974 (5.65c+CU/IDA-1.4.4/HLK for chemistry@ccl.net); Fri, 27 Aug 1993 08:38:23 -0400 Received: from still3.chem.columbia.edu by merhaba.cc.columbia.edu with SMTP id AA12372 (5.65c+CU/IDA-1.4.4/HLK for GDURST%elinet1.dowelanco.com@cunixf.cc.columbia.edu); Fri, 27 Aug 1993 08:36:25 -0400 Received: by still3.chem.columbia.edu (920330.SGI/920502.SGI.AUTO) for @cunixf.cc.columbia.edu:chemistry@ccl.net id AA14894; Fri, 27 Aug 93 08:38:12 -0400 Date: Fri, 27 Aug 93 08:38:12 -0400 From: shenkin@still3.chem.columbia.edu (Peter Shenkin) Message-Id: <9308271238.AA14894@still3.chem.columbia.edu> To: "Gregory L. Durst - DowElanco Discovery Research" , chemistry@ccl.net Subject: Re: IRIX 5.0.1 & MOPAC 6.0?? Cc: GDURST@elinet1.dowelanco.com > From: "Gregory L. Durst - DowElanco Discovery Research" > We recently upgraded one of our SGI servers to an Onyx running IRIX 5.0.1 > and have seen a problem running MOPAC 6.0 with ESP options compiled in. > Now when we run a MOPAC job, the machine is unable to execute any > other programs. Things just won't run! Never seen anything like this before. > Errors appear in the console window stating things like: > > NOTICE: dupreg - temporarily insufficient memory to allocate virtual swap space, > process buttonfly [1592] > > OR > > NOTICE: growreg - temporarily insufficient memory to expand region, process > sybyl [1596] > > This does *not* happen on our other SGI server running IRIX 4.0.5... This is probably a consequence of the way SGI allocates memory under IRIX 5.0.1. The differences between IRIX 3.x.x and 4.x.x in this regard were discussed in the comp. chem. list a few weeks ago. IRIX 5.x.x changes the paradigm again. I don't know the 5.x.x paradigm as well as the other two, but my understanding is as follows: 3.x.x: On process startup (or at malloc time, for processes that use malloc), reserve as much swap+RAM as the total size of the program. This guarantees that any memory allocated will be available if/when used, but is wasteful for Fortran programs that allocate array space for large data sets that are rarely encountered. 4.x.x: Reserve swap+RAM for a memory location when an attempt is made to access it -- not when memory is declared or malloc'ed by the process. This makes for higher efficiency of resource use, but is non-deterministic: a program can be killed in mid- execution if some process (not necessarily itself!) all of a sudden tries to access array elements that the system can't find physical resources for. The OS then has to kill some process, and usually selects the largest -- which on occasion may be the X-server :-(. 5.x.x: Reinstate the 3.x.x behavior, but allow the system administrator to declare an arbitrary amount of "virtual swap space. If this amount is zero, then we get exactly the 3.x.x behavior. If it is high, then we get some approximation to the 4.x.x behavior. (4.x.x has essentially infinite virtual swap space.) Though the precise nature of your difficulty is not clear to me from the wording of your error messages, it may be that what you need to do is allocate more virtual swap space. See the manual entry on "swap -v" for a description and a brief discussion of this. The man page suggests that you "SEE ALSO" swapctl(2). My manual doesn't have an entry for this, but the name would suggest that it allows a process to control the allocation of (virtual?) swap space for itself. It is also possible that you simply don't have enough "real" swap space on your Onyx to run these presumably very large programs. You can see how much swap space you have on either your Onyx or your 4.x.x system by issuing the command "swap -l". Certainly your real swap space should be at least as large on the Onyx as on your 4.x.x system. If it isn't, increase it. If it is, add virtual swap space. If you've been happy with the indeterminate allocation method on the 4.x.x server, you ought to add an effectively infinite amount of swap space to the 5.x.x Onyx. -P. ************************f*u*cn*rd*ths*u*cn*gt*a*gd*jb************************ Peter S. Shenkin, Box 768 Havemeyer Hall, Dept. of Chemistry, Columbia Univ., New York, NY 10027; shenkin@still3.chem.columbia.edu; (212) 854-5143 ********************** Wagner, Beame, Screvane in '93! ********************** From DSMITH@uoft02.utoledo.edu Fri Aug 27 05:01:04 1993 Received: from uoft02.UTOLEDO.EDU for DSMITH@uoft02.utoledo.edu by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA25028; Fri, 27 Aug 1993 10:01:18 -0400 Received: from UOFT02.UTOLEDO.EDU by UOFT02.UTOLEDO.EDU (PMDF V4.2-10 #3438) id <01H28IB7RDVK001END@UOFT02.UTOLEDO.EDU>; Fri, 27 Aug 1993 10:01:04 EST Date: Fri, 27 Aug 1993 10:01:04 -0500 (EST) From: "DR. DOUGLAS A. SMITH, UNIVERSITY OF TOLEDO" Subject: second post: JT vs. doublet instability To: chemistry@ccl.net, mmodinfo@uoft02.utoledo.edu, hyperchem@autodesk.com Message-Id: <01H28IB7SQ3M001END@UOFT02.UTOLEDO.EDU> X-Envelope-To: chemistry@ccl.net X-Vms-To: CHEMISTRY, MMODINFO, HYPERCHEM Mime-Version: 1.0 Content-Transfer-Encoding: 7BIT A while back I posted this to the net; suprisingly and disappointingly, I received absolutely no replies. So, I would like to try again. In a recent paper (J. Org. Chem. 1993, 58, 6) we reported on the geomietric distortion of the triplet nitrenium ion derived from azepine (C6H6N+), although we could not distinguish between Hartree-Fock doublet instability and vibronic coupling-induced pseudo Jahn Teller distortion as the cause. In trying to sort this out, I have several questions to put to the readership of this mailing list. 1. In other azaaromatic systems such as pyridine and pyrimidine, vibronic coupling of low lying triplet states is invoked as the reason for geometric distortions. These distortions are out-of-plane deformations, as opposed to the in-plane distortion we observed in the azepine system. Is this because the two former systems are six-membered rings while azepine is a seven atom heterocycle? 2. Are there any examples of vibronic coupling-induced geometric distortions for other homoaromatic systems, e.g. tropylium? If so, are these in-plane or out-of-plane distortions? 3. Are there any examples of vibronic coupling-induced geometric distortions for three-membered ring aromatic systems, e.g. cyclopropenyl cation? This system would necessarily be planar, so any distortion should be (IMHO) in-plane. 4. In the absence of experimental data, how does one computationally determine the existence of vibronic coupling? From my reading of the literature (e.g. Buma, et al., J. Am. Chem. Soc. 1992, 114, 9544) I cannot see how coupling is unambiguously determined. In the paper cited, the authors calculated several low lying excited triplet states and examined the normal mode frequencies,then they correlated the direction of the geometric distortions in each state. This somehow led them to the conclusion that vibronic coupling was occuring. (I am only an organic chemist, their arguments just don't make enough sense to me.) Can someone help explain this to me? 5. Furthermore, the explanation by these authors based on electronic structure ("We argue that an azabenzene in an npi* state may well be susceptible to out-of-plane distortions because the pi-electron system in this kind of molecules [sic] becomes in first approximation a 7-pi-electron system and thus is no longer aromatic.") seems to me to be just handwaving of the type an organic chemist would use. The explanation seems empirically valid but does not really explain anything, especially in light of our results for the azepine system. On the other hand, if this explanation really is valid, then perhaps our azepine results are due to HF doublet instability rather than vibronic coupling. Help! 6. These authors also use energetic arguments that don't seem to me to "prove" vibronic coupling. For example, "The excitation to the 3A2(npi*) state... results in a large out-of-plane distortion of the C2-H7 fragment with a large stabilization energy, indicating that the vibronic coupling between the 3A2(npi*) and 3B2(pipi*) states is considerably stronger than the vibronic coupling between the 3B1(npi*) and 3A1(pipi*) states [where the stabilization energy was small]." This sounds like circular reasoning to me, i.e. vibronic coupling exists because there is a large stabilization energy due to vibronic coupling. Or am I missing the point? On a related topic, another question. When doing a CASSCF calculation on a triplet state of any molecule, is it absolutely necessary to include both unpaired electrons and both singly occupied orbitals (and their corresponding antibonding orbitals)? In particular, when calculating the triplet state of a nitrenium ion, should the two unpaired electrons formally on the nitrogen be tightly coupled or correlated? Please direct replies to the net, in order to foster discussion and further insights. Doug Douglas A. Smith Assistant Professor of Chemistry and of Medicinal and Biological Chemistry The University of Toledo Toledo, OH 43606-3390 voice 419-537-2116 fax 419-537-4033 email dsmith@uoft02.utoledo.edu From msjones@whale.st.usm.edu Sat Aug 28 36:10:37 1993 Received: from whale.st.usm.edu for msjones@whale.st.usm.edu by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA01452; Fri, 27 Aug 1993 11:56:13 -0400 Received: by whale.st.usm.edu (AIX 3.2/UCB 5.64/4.03) id AA08599; Fri, 27 Aug 1993 10:54:37 -0500 From: msjones@whale.st.usm.edu (Michael Sean Jones) Message-Id: <9308271554.AA08599@whale.st.usm.edu> Subject: Grad Schools To: CHEMISTRY@ccl.net (chemlist) Date: Fri, 27 Aug 1993 10:54:37 +22304916 (CDT) X-Mailer: ELM [version 2.4 PL20] Content-Type: text Content-Length: 695 Netters, I am interested in applying to graduate school in the discipline of computational chemistry. I am very eager to work on biological macromolecules. I am requesting a list of as many grad schools as possible that offer this type of degree. I would also be interested in a list of companies that are actively engaged in this sort of research. I am interested in making some sort of contacts in industry in order to more appropriately direct my research. Any help would be greatly appreciated. Thanks in advance. Michael S. Jones Univesity of Southern Mississippi Department of Chemistry and Biochemistry Internet: msjones@whale.st.usm.edu or msjones@wave.st.usm.edu From DFAC@ANDESCOL.UNIANDES.EDU.CO Fri Aug 27 13:29:42 1993 Received: from phem3 (phem3.acs.ohio-state.edu) for DFAC@ANDESCOL.UNIANDES.EDU.CO by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA03086; Fri, 27 Aug 1993 13:08:16 -0400 Received: from ANDESCOL.UNIANDES.EDU.CO (MAILER@ANDESCOL) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #3557) id <01H28OWMO9CG8X244V@phem3.acs.ohio-state.edu>; Fri, 27 Aug 1993 13:08:08 EDT Received: from ANDESCOL (DFAC) by ANDESCOL.UNIANDES.EDU.CO (Mailer R2.10 ptf000) with BSMTP id 3592; Fri, 27 Aug 93 11:49:24 COL Date: Fri, 27 Aug 93 11:49:06 COL From: Alex Jaimes Subject: Heat Pumps To: chemistry@ccl.net Message-Id: <01H28OWMO9CI8X244V@phem3.acs.ohio-state.edu> Content-Transfer-Encoding: 7BIT Hi.... I'm looking for information on Heat Pumps - the types that exist and their many applications. If you know of any application (even if it's an ~obvious~ one) or know of anyone who knows about it or has info on this topic, I would greatly appreciate it if you'd let me know. Any info (including places where I can look) is welcome. I'm not subscribed to the list, so please answer me directly. Thanks a lot, Alex Jaimes Los Andes University - Bogota, Colombia S.A. DFAC (Computer Aided Manufacturing and Design Research Group) e-mail: DFAC@ANDESCOL From steve@onsager.chem.columbia.edu Fri Aug 27 10:18:10 1993 Received: from onsager.chem.columbia.edu for steve@onsager.chem.columbia.edu by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA05690; Fri, 27 Aug 1993 14:19:05 -0400 Received: by onsager.chem.columbia.edu (AIX 3.2/UCB 5.64/4.03) id AA16819; Fri, 27 Aug 1993 14:18:10 -0400 Date: Fri, 27 Aug 1993 14:18:10 -0400 From: steve@onsager.chem.columbia.edu (Steve Stuart) Message-Id: <9308271818.AA16819@onsager.chem.columbia.edu> To: chemistry@ccl.net Subject: Re: MD On a note related to the solvent MD question: Does anyone know of any work that has been done on simulating proteins using a *polarizable* water model? -Steve Stuart steve@onsager.chem.columbia.edu From hogue@calumet.den.mmc.com Fri Aug 27 11:11:28 1993 Received: from calumet.den.mmc.com for hogue@calumet.den.mmc.com by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA00732; Fri, 27 Aug 1993 11:11:24 -0400 Received: by calumet.den.mmc.com (4.1/1.34.a) id AA02529; Fri, 27 Aug 93 09:11:24 MDT Date: Fri, 27 Aug 93 09:11:24 MDT From: hogue@calumet.den.mmc.com (Pat Hogue 1-2183) Message-Id: <9308271511.AA02529@calumet.den.mmc.com> To: chemistry@ccl.net Subject: Heavy Fermions Status: RO Has anyone successfully modeled the heavy fermion or Hondo effect? From stoutepf@chemsci1.es.dupont.com Fri Aug 27 10:41:44 1993 Received: from gatekeeper.es.dupont.com for stoutepf@chemsci1.es.dupont.com by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA10452; Fri, 27 Aug 1993 16:25:59 -0400 Received: by gatekeeper.es.dupont.com (5.65/ULTRIX-mjr-062991); id AA16914; Fri, 27 Aug 93 15:42:20 -0400 Received: from [138.196.64.95] (chem95.es.dupont.com) by chemsci1.es.dupont.com. chemsci1 chemsci1.es.dupont.com (4.1/SMI-4.1) id AA25522; Fri, 27 Aug 93 15:41:15 EDT Message-Id: <9308271941.AA25522@chemsci1.es.dupont.com. chemsci1 chemsci1.es.dupont.com> Reply-To: stoutepf@chemsci1.es.dupont.com X-Organization: The Du Pont Merck Pharmaceutical Company X-Mailer: Eudora 1.3.1 Date: Fri, 27 Aug 1993 15:41:44 -0500 To: CHEMISTRY@ccl.net From: stoutepf@chemsci1.es.dupont.com (Pieter Stouten) Subject: MD with water ... On Fri, 27 Aug 93 13:37, Arne Elofsson wrote: >the solvent effect can be reproduced >rather well with specific solvent potentials but >they seem to be slower than to include specific >waters. (Chris Sander had a paper in last J.M.B >with something that sounded very fast.) > I am not completely sure, but somehow doubt that it was published in J.M.B. :-). Also, effective solvation can be much faster than using explicit water. Our method is only 20-50% (20% in PRESTO, 50% in GROMOS) slower than VACUUM simulations. The reference is: P.F.W. Stouten, C. Froemmel, H. Nakamura & C. Sander, "An Effective Solvation Term Based on Atomic Occupancies for Use in Protein Simulations," Mol. Simulation 10 (1993) 97-120. Cheers, Pieter. Pieter Stouten, Senior Research Scientist || Computer Aided Drug Design Group || The Du Pont Merck Pharmaceutical Company || Adventures get spoiled P.O. Box 80353, Wilmington, DE 19880-0353 || by being reduced to data Phone: +1 (302) 695 3515 || -- Fax: +1 (302) 695 2813 || Poul Anderson ARA/Fax: +1 (302) 695 4324 || E-mail: stoutepf@chemsci1.es.dupont.com || E-mail: stoutepf@lldmpc.dnet.dupont.com || From ryszard@MSI.COM Fri Aug 27 13:17:01 1993 Received: from schizoid.msi.com for ryszard@MSI.COM by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA11847; Fri, 27 Aug 1993 17:17:28 -0400 Received: from hogan.MSI.COM by schizoid.msi.com (4.1/SMI-4.1) id AA17219; Fri, 27 Aug 93 17:17:04 EDT Received: by hogan.MSI.COM (AIX 3.2/UCB 5.64/4.03) id AA13848; Fri, 27 Aug 1993 17:17:01 -0400 Date: Fri, 27 Aug 1993 17:17:01 -0400 From: ryszard@msi.com (Ryszard Czerminski X 285) Message-Id: <9308272117.AA13848@hogan.MSI.COM> To: DSMITH@uoft02.utoledo.edu, chemistry@ccl.net, hyperchem@autodesk.com, mmodinfo@uoft02.utoledo.edu Subject: Re: second post: JT vs. doublet instability Doug: Probably this reference will not answer your questions directly, but you might find it usefull... A. Sobolewski, R. Czerminski "The Potential Energy Surfaces and the Radiationless Dynamics of Excited States of Benzene and Pyridazine" Chem. Phys. 130, 123 (1989) Ryszard Czerminski Molecular Simulations 16 New England Executive Park, Burlington, MA 01803-5297 phone: (617)229-8875 x 217 fax: (617)229-9899 e-mail: ryszard@msi.com From raman@bioc01.uthscsa.edu Fri Aug 27 14:35:40 1993 Received: from thorin.uthscsa.edu for raman@bioc01.uthscsa.edu by oscsunb.ccl.net (5.65c+KVa/930601.1506) id AA15812; Fri, 27 Aug 1993 21:48:08 -0400 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Fri, 27 Aug 1993 20:48:36 -0500 (CDT) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA05852; Fri, 27 Aug 93 19:35:44 CDT From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9308280035.AA05852@bioc01.uthscsa.edu> Subject: Accessible Surface Areas... To: chemistry@ccl.net Date: Fri, 27 Aug 1993 19:35:40 -0500 (CDT) X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 1276 Dear netters: Is anyone aware of an algorithm that can compute polar and non-polar solvent accessible surface areas for a PARTIAL MOLECULAR SURFACE, i.e. a region of approximately 1000 square angstroms around a particular residue in a protein? I am not familiar with a program that does it and do know that both ACCESS and the MSP suite do not implement this. Before I write my own code to do the same, I was wondering if someone had already done this? I would appreciate a quick response on this matter. Cheers -raman -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry c.raman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ******************************************************************************