From a283212@lrzpc10174.lrz-muenchen.de Fri Jan 23 03:16:53 1998 Received: from sunsrv5.lrz-muenchen.de for a283212@lrzpc10174.lrz-muenchen.de by www.ccl.net (8.8.3/950822.1) id CAA26740; Fri, 23 Jan 1998 02:53:43 -0500 (EST) Received: from lrzpc10174.lrz-muenchen.de by sunsrv5.lrz-muenchen.de; Fri, 23 Jan 98 08:53:39 +0100 Received: by lrzpc10174.lrz-muenchen.de (NX5.67e/NX3.0S) id AA00857; Fri, 23 Jan 98 08:53:38 +0100 Message-Id: <9801230753.AA00857@lrzpc10174.lrz-muenchen.de> Mime-Version: 1.0 (NeXT Mail 3.3 v118.2) Content-Type: multipart/alternative; boundary=NeXT-Mail-801923790-14 Content-Transfer-Encoding: 7bit X-Image-Url: ftp://ftp.imo.physik.uni-muenchen.de/pub/Images/heller.tiff X-Face: #K8+M!=vK|\bQ[&P:z)d$Q:i(@36P1!7if~nI%OB\9I>;p5Vs<_YkU;].K(chZJ,k8X96t ]!d?;H/|Jc:Hr-hhbBow![@FkT0xNOVXK|TO%Jg@Xz Date: Fri, 23 Jan 98 08:53:37 +0100 To: root Subject: Re: RANToid:RFC: pdb ; perl ; cgi-bin ; a MD box initial state build question Cc: chemistry@www.ccl.net Reply-To: Helmut.Heller@lrz-muenchen.de X-Reply-Format: NeXT Mail preferred X-Url: http://www.lrz.de/~heller --NeXT-Mail-801923790-14 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable I got a message that there was an error and my posting could not be = transmitted, so I am trying again! Helmut Dear Eugene , You wrote: > The only thing short of absolute bliss would be a salt script, which > mutates a provided number of waters into, say, Na+Cl- pairs. Easy in = perl, > again. While you are downloading EGO, also get a friend of it, namely Solvate = from Helmut Grubm=FCller: [An attachment was originally included = here]http://www.mpibpc.gwdg.de/abteilungen/071/solvate.html It is much more advanced than my simple FORTRAN program AND it can place = ions around your protein/lipid of interest. And, after all, it works = nicely together with EGO [An attachment was originally included = here]:-)[An attachment was originally included here] > Next step to be taken, is building a lipid bilayer from above lego = blocks > (Helmut used Quanta, which afair is not free). I was thinking about > writing tlate-x , tlate-y , and mirror-z , With the EGO distribution comes a nifty utility, pdbpatch, which was = written by Marcus Eichinger, and which does just that! Call it without = parameters to get a basic usage summary. In interactiv mode type help for = more info. > (Btw, those of you who are eying DIY DSP-fueled MD > systems, should definitely check out Helmut Heller's (1993) Ph.D. work > (which, afaik, is unfortunately only available in German), as it = contains > yummy details about doing MD on a 60-node 4 MByte/node DIY Inmos > Transputer box). Thank you very much for this great recommendation[An attachment was = originally included here]:-)[An attachment was originally included here] = While what you say about the German part is undoubtedly true, we = published, out of Helmut Grubm=FCller's and my thesis, a paper in = Molecular Simulation which is in English and should be a bit more = accessible: @ARTICLEHELL90, author=3DHelmut Heller and Helmut Grubm"uller and Klaus Schulten, title=3DMolecular Dynamics Simulation on a Parallel Computer, journal=3DMS, volume=3D5, year=3D1990, pages=3D133--165, reference=3DPub.#~111 > Unfortunately, these are neutral > lipids, while my work is supposed to be about polycation-induced (btw, > polyelectrolyte MD also many CCL search hits do not make) lateral > segregation. What to do? Well, my first idea was just cut off that pesky > choline tail of some lipids (for chaperoning sake, interdigitating them > with neutral ones), and compensate one of the negative charges with, = say, > Na+. I think this can be done with X-PLOR (which is, imho, quite an > intimidating package), RasMol, or a one-time (perl) script. What is your > personal preference? I prefer to do such things with X-PLOR and I have some scripts (e.g., = POPC2DPPC.inp) which I could put on my WWW pages (which, btw., have moved = (and so have I [An attachment was originally included here];-)[An = attachment was originally included here] to a new location: [An attachment = was originally included here]http://www.lrz.de/~heller, new email: = heller@lrz.de) if there is some interest in them. Just let me know. I hope this helps a bit, later, Helmut P.S.: [An attachment was originally included = here]http://liposome.genebee.msu.su/cgi-bin/test did not work for me [An = attachment was originally included here]:-([An attachment was originally = included here] --- Servus, Helmut (DH0MAD) ______________NeXT-mail = welcome_________________ FAX: +49-89-280-9460 " Knowledge must be gathered and cannot be = given " heller@lrz.de ZEN, one of BLAKES7 Phone: +49-89-289-28823 = ----------------------------------------------------------------------------= ------- Dr. Helmut Heller =20 Leibniz-Rechenzentrum (LRZ) =20 High Performance Computing Group Barer Str. 21, Zi S2515, 80333 Munich, GERMANY =20 --NeXT-Mail-801923790-14 Content-Type: text/enriched; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable I got a message that there was an error and my posting could not be = transmitted, so I am trying again! Helmut Dear Eugene , You wrote: > The only thing short of absolute bliss would be a salt script, which > mutates a provided number of waters into, say, Na+Cl- pairs. Easy in = perl, > again. While you are downloading EGO, also get a friend of it, namely Solvate = from Helmut Grubm=FCller: Next step to be taken, is building a lipid bilayer from above lego = blocks > (Helmut used Quanta, which afair is not free). I was thinking about > writing tlate-x <, tlate-y <, and mirror-z <, With the EGO distribution comes a nifty utility, pdbpatch, which was = written by Marcus Eichinger, and which does just that! Call it without = parameters to get a basic usage summary. In interactiv mode type help for = more info. > (Btw, those of you who are eying DIY DSP-fueled MD > systems, should definitely check out Helmut Heller's (1993) Ph.D. work > (which, afaik, is unfortunately only available in German), as it = contains > yummy details about doing MD on a 60-node 4 MByte/node DIY Inmos > Transputer box). Thank you very much for this great recommendation <:-) < While what you say about the German part is undoubtedly true, we = published, out of Helmut Grubm=FCller's and my thesis, a paper in=20 Molecular Simulation which is in English and should be a bit more accessible: @ARTICLEHELL90, author=3DHelmut Heller and Helmut Grubm"uller and Klaus Schulten, title=3DMolecular Dynamics Simulation on a Parallel Computer, journal=3DMS, volume=3D5, year=3D1990, pages=3D133--165, reference=3DPub.#~111 > Unfortunately, these are neutral > lipids, while my work is supposed to be about polycation-induced (btw, > polyelectrolyte MD also many CCL search hits do not make) lateral > segregation. What to do? Well, my first idea was just cut off that pesky > choline tail of some lipids (for chaperoning sake, interdigitating them > with neutral ones), and compensate one of the negative charges with, = say, > Na+. I think this can be done with X-PLOR (which is, imho, quite an > intimidating package), RasMol, or a one-time (perl) script. What is your > personal preference? I prefer to do such things with X-PLOR and I have some scripts (e.g., = POPC2DPPC.inp) which I could put on my WWW pages (which, btw., have moved = (and so have I=20 <;-) < to a new location:=20 ; Fri, 23 Jan 1998 10:55:01 +0100 (MET) Received: from cerbere.limeil.cea.fr (cerbere.bruyeres.cea.fr [132.165.76.1]) by muguet.saclay.cea.fr (8.8.8/CEAnet-relay-4.0.3) with SMTP id KAA17265 for ; Fri, 23 Jan 1998 10:55:01 +0100 (MET) Received: by cerbere.limeil.cea.fr (CEANET-1.1+) id AA24890; Fri, 23 Jan 1998 10:53:53 +0100 Received: from indre.ripault.cea.fr(132.165.32.1) by cerbere via smap id sma024884; Fri Jan 23 10:53:32 1998 Received: from ripault.cea.fr (cher.ripault.cea.fr [132.165.32.3]) by ripault.cea.fr. (8.8.5/8.7.3) with ESMTP id KAA09854 for ; Fri, 23 Jan 1998 10:53:37 +0100 Received: from cher.ripault.cea.fr (localhost [127.0.0.1]) by ripault.cea.fr (8.8.4/8.7.3) with SMTP id KAA01499 for ; Fri, 23 Jan 1998 10:54:17 +0100 Sender: mathieu@ripault.cea.fr Message-Id: <34C868C9.62660454@ripault.cea.fr> Date: Fri, 23 Jan 1998 10:54:17 +0100 From: Didier MATHIEU Organization: CEA - Le Ripault X-Mailer: Mozilla 3.0 (X11; I; Linux 2.0.18 i586) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: SUMMARY: QEq charges & applications References: <9801151456.AA145133@rzurs10.unizh.ch> Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Dr. S. Shapiro & Bakowies, Here are relevant responses to my inquiry about QEq charges and their applications: ******** "Andrey Bliznyuk" I spent some time trying to apply different versions of Qeq / PEOE methods. I even add some more parameters and tried to optimize them in order to reproduce charges, obtained from electroststaic potential calculations. Results been disappointing. I come to conclusion that you need many special atom types in order to get reasonable results. On the other hand, if you are ready to live with not very accurate potential (charges in that case may differ substantially, for example by 0.2 a.u.), these methods may be useful. > In this context, maybe it would be better to transfer atomic charges > derived for chemical groups, between molecules showing the same > chemical structures ? The main reason I was looking for QEq charges was that the results obtained from coventional MM calculations were unsutisfactory. > I don't know exactly how accurate atomic charges should be. I want > to use them to derived molecular indexes, from averages of the > electrostatic potential over molecular surfaces. For instance, I'd > like to find relationships between sublimation enthalpy of molecular > materials and such indexes. Because such empirical relations are not > expected to be accurate maybe I could be satisfy with QEq charges I guess, that it should work for you. ******** "Smith JA (Jack)" A simple idea I've been toying with is the use of Rappe's QEq scheme (perhaps coupled with Landis' VALBOND scheme) together with a variationally derived analytical Thomas-Fermi expression for the charge density of charged atoms. This generates a very quick, crude, but surprisingly good electron density (a superposition of charged atom densities) and a full electrostatic potential (in analytical form) corresponding to the QEq charges. It's fast enough to perform at an MD timescale. > I would be eager to know more about your "toy". > I say 'toy' because I don't get much opportunity to actually work on this stuff. > > (perhaps coupled with Landis' VALBOND scheme) > > Do you please have any reference about this Landis'VALBOND scheme ? > The following was posted by Clark (landis@piggy.chem.wisc.edu) to another list where VALBOND was being discussed (BTW, Dan Root now works for MSI): Published VALBOND work includes: 'Valence Bond Concepts Applied to the Molecular Mechanics Description of Molecular Shapes 1. Application to Non-hypervalent Molecules of the P-block.' Daniel M. Root, Clark R. Landis, and Thomas Cleveland, J. Am. Chem. Soc., 1993, 115, 4201-4209. 'Valence Bond Concepts, Molecular Mechanics Computations, and Molecular Shapes' Clark R. Landis, Advances in Molecular Structure Research, Vol. 2, Magdolna Hargittai and Istvan Hargittai, Editors, JAI Publishers, Inc. New York, 1995. 'Making Sense of the Shapes of Simple Metal Hydrides' Clark R. Landis, Thomas Cleveland, Timothy K. Firman, J. Am. Chem. Soc., 1995, 117, 1859-1860. 'Regarding the Structure of W(CH3)6' Clark R. Landis, Thomas Cleveland, and Timothy K. Firman, Science, 1996, 272, 179. 'Valence Bond Concepts Applied to the Molecular Mechanics Description of Molecular Shapes. 2. Applications to Hypervalent Molecules of the P-Block', Tom Cleveland and Clark R. Landis, J. Am. Chem. Soc.,1996, 118, 6020-6031. 'Steric Effects in the Cleavage of Dinitrogen by Molybdenum Triamide Complexes', Konstantin Neyman, Jutta Hahn, Notker Rösch, and Clark R. Landis, Inorganic Chemistry; 1997; 36; 3947-3951. > > variationally derived analytical Thomas-Fermi expression for the > charge > > density of charged atoms. > > Do you mean you solve the Euler equations for Thomas-Fermi under the > constraint that atomic charges (defined in which way ?) should equal > QEq > charges ? > The analytical TF work actually dates back to that of Peter Csavinsky [Phys Rev 166, 53 (1968); Phys Rev 8A, 1688 (1973)]. I use his analytical expression (or some DZP-like extension of it) for the nuclear screening function, separate out the pure Z/R term, and substitute a QEq-adjusted N (N-q) for the number of electrons in the N*phi(x)/R term (where phi is the screening function and x is the universal TF coordinate). > Or you simply modify the expression for the electrostatic potential > according to such charges, but I cannot see how it can be done in a > consistent way ? > The potential would simply be Z/R - (Z-q)*phi(x)/R where q is the partial charge adjustment (from QEq, for example) and phi(x) is the universal (Z-dependent) screening function. In my own methodology, though, the screening function is refit dynamically to match the GC-UHF Coulomb potential for each atom in a self-consistent atoms-in-molecules approach. This amounts to decomposing the molecular UHF Coulomb potential (plus nuclear attraction) into a superposition of atomic TF-like potentials. > Finally, it seems you were interested mostly in the electron density, > Actually I'm in a variety of aspects. I just found that I could generate a quick and dirty density (mainly for generating density isosurfaces for visualization purposes) as a superposition of charge-adjusted TF densities. In TF theory, the potential is directly related to the density, though. > while I am only concerned - in a first approach - with the molecular > electrostatic potential. Do you think the MEP derived for your TF > density for charged atoms is better than the MEP obtained from the > coulombic interaction with QEq charges ? > What this gives you is a screened potential at each atomic site instead of point charges. So it would be more like a density derived MEP. I don't know if would actually be any better in practice, but I'd think it's worth a try. Point charge models always bother me. Atomic partial charges (especially Mulliken type) also bother me. Since QEq charges are derived from matching chemical potentials between atoms (no arbitrary basis partitioning) and the TF screening maps this to a density, I feel much more comfortable with it. However, I have no real experience in trying to use these for real problems - it's still only a 'toy'. > What do you mean by a > "potential CORRESPONDING to QEq charges"... are they essentially the > same ? > No. The TF (screened Coulomb) potential is not a point charge model. The nuclear charge is localized (Z/R), but the electronic charge has more of a Q*exp(R)/R behavior. I suppose one could fit a point charge model to the resulting potential, but why? ******** bakowies@brok.ucsf.EDU (Dirk Bakowies) some time ago we have reported a semiempirical implementation of Rappe and Goddard's QEq scheme. With MNDO type formulas for the two-center integrals, we have calibrated the model to reproduce either Mulliken or potential derived charges. It turns out that Mulliken charges are easier reproduced (typically 0.05 e off) than potential derived charges (0.1 e off). For standard organic molecules the scheme proved accurate enough to be used in hybrid QM/MM calculations. It is my experience, however, that subtle charge shifts due to electron delocalization are not captured by the model. See: D. Bakowies, W. Thiel; J. Comp. Chem. 17 (1996) 87, JPC 100 (1996) 10580. ******** goto@msi.com (Narushi Goto) Indeed I did some calculation using QEq to estimate IR/Raman spectrum. As you already know, the frequencies are depend on the accuracy of force field parameter. So in some case, I could estimate frequencies and intensities with very high accuracy, but in some case I could not. Finally, in my opinion, QEq method is very good to calculate the charges in a short time. Why don't you contact the Caltech Staff? ******** John McKelvey A thought about the reliability of Qeq related to chemical shifts, etc: The way I read the paper is that Qeq is built on the coulombic interactions of the CNDO Hamiltonian.... ******** -- Didier MATHIEU CEA - Le Ripault, BP 16 37260 Monts (France) Tel. 33(0)2.47.34.41.85 From pino@jsbach.dichi.unina.it Fri Jan 23 10:16:54 1998 Received: from jsbach.dichi.unina.it for pino@jsbach.dichi.unina.it by www.ccl.net (8.8.3/950822.1) id JAA29208; Fri, 23 Jan 1998 09:54:04 -0500 (EST) From: Received: by jsbach.dichi.unina.it (AIX 3.2/UCB 5.64/4.03) id AA11305; Mon, 6 Jun 1994 15:48:21 GMT Date: Mon, 6 Jun 1994 15:48:21 GMT Message-Id: <9406061548.AA11305@jsbach.dichi.unina.it> To: CHEMISTRY@www.ccl.net Subject: Volume of Molecular Cavities Dear netters, I would appreciate to receive informations about programs and algorithms able to detect cavities and evaluate their volume and dimension. Please, send me literature and informations about programs. Thanx in advance Pino =========================== Pino Milano Universita' degli Studi di Salerno Baronissi (ITALY) e-mail pino@jsbach.dichi.unina.it =========================== From root@liposome.genebee.msu.su Thu Jan 22 10:16:42 1998 Received: from liposome.genebee.msu.su for root@liposome.genebee.msu.su by www.ccl.net (8.8.3/950822.1) id JAA22704; Thu, 22 Jan 1998 09:31:09 -0500 (EST) Received: from localhost (root@localhost) by liposome.genebee.msu.su (8.8.5/8.8.5) with SMTP id RAA14097; Thu, 22 Jan 1998 17:37:14 +0300 Date: Thu, 22 Jan 1998 17:37:13 +0300 (MSK) From: root Reply-To: root To: chemistry@www.ccl.net Subject: RANToid:RFC: pdb ; perl ; cgi-bin ; a MD box initial state build question Message-ID: Dear CCLers, I am slowly catching up with that treasure trove of information contained in the archives, however -- I may well be mistaken -- but the interactive webform-driven aspects of cgi-bin perl script pdb generation are not very well covered. As, for personal-belief and for financial reasons both I am sticking to freely obtainable software, some apparently simple problems must (un?)necessarily appear nontrivial (which is worsened by my lack of experience in the field, and the unavailability (but then I think I saw at least two different CCL search hits from my own domain...) of local experts -- Please help me, Obi Wan! ;) >From all free parallel MD software I tested so far, I finally decided to stick to EGO: ftp://ftp.imo.physik.uni-muenchen.de/pub/ego/ http://www.imo.physik.uni-muenchen.de/tavan/molgroup/ego_manual/manual.html NAMD does still appear interesting (I'll sure come back to check later, esp. NAMD2), particularly its advanced features like DMTA, the video-game-like ;) VMD/NAMD coupling, but, perhaps unjustified, I found it less easy to use. (Btw, those of you who are eying DIY DSP-fueled MD systems, should definitely check out Helmut Heller's (1993) Ph.D. work (which, afaik, is unfortunately only available in German), as it contains yummy details about doing MD on a 60-node 4 MByte/node DIY Inmos Transputer box). Well, I got somewhat sidetracked, and my X-PLOR(online) is not up yet, so I still cannot pdb2psf, but I got a nice visual feedback by VMD replaying a DMD generated from a demo dataset (bovine trypsine inhibitor) that comes bundled with EGO. The in vacuo protein in question was small (cat pti.pdb | grep 'ATOM ' | wc claims 568 ATOMs), but I could render roughly half a nanosecond worth of trajectory in (probably much) less than 24 h on a measly single-node AMD K6/200 (roughly 400 BogoMIPS), which is not exactly known for its float performance being stellar. (Them remote Indys ain't that either, the PVM's still not quite right, the network topology is distintly suboptimal, and I'll soon break down, and start crying ;). Helmut Heller (very helpful, thanks Helmut!) published a phospholipid modeler's basic survival kit of hydrated phospholipid coordinates (both initial (fake crystal), and final (well-equilibrated) state) at: ftp://ftp.imo.physik.uni-muenchen.de/pub/membrane/ (Anybody knows, where to obtain Terry Stouch's relatively recent (dimyristoylphoshatidylcholine) set?). Unfortunately, these are neutral lipids, while my work is supposed to be about polycation-induced (btw, polyelectrolyte MD also many CCL search hits do not make) lateral segregation. What to do? Well, my first idea was just cut off that pesky choline tail of some lipids (for chaperoning sake, interdigitating them with neutral ones), and compensate one of the negative charges with, say, Na+. I think this can be done with X-PLOR (which is, imho, quite an intimidating package), RasMol, or a one-time (perl) script. What is your personal preference? Another (demented) idea was to build a coordinate set de novo. I believe I already mentioned Daylight's SMILES strings (which, apart from being constructable manually, e.g. using the interactive web form depict facility) can be easily drawn using Gasteiger's Cactvs suite (csed), and sent to Corina http://schiele.organik.uni-erlangen.de/cactvs/index.html (1 k free structures for everybody!) via email for an overnight crunch, http://schiele.organik.uni-erlangen.de/services/3d.html the results (hopefully) arriving in the morning mail. Maybe complicated, but it works for me. Alas, the coordinate come trivially minimalized, which, especially in case of phospholipids is definitely not what I want. Any ideas about how to rotate individual bonds, maybe (dream on) interactively? Next step to be taken, is building a lipid bilayer from above lego blocks (Helmut used Quanta, which afair is not free). I was thinking about writing tlate-x , tlate-y , and mirror-z , then maybe strip-tip3p (RasMol can do this), and fuse-pdb (fusing two coordinate sets into one), maybe starting with Will Ware's work here: http://world.std.com/~wware/ (he has a link to some nifty subpage illustrating his early structure-building (gcl & scheme) Lisp code buried there somewhere), porting it to Emacs' elisp (which would weird out too many people), or, better, to perl, which would have the nice cgi-bin synergy. What do you think of this scheme? Got perhaps even pointers to ready code? There is some fortran utility (compiles with f77, also, after updating several packages with RedHat's fort77 (which is a front-end to f2c)) which comes bundled with EGO, which can cubic-primitive-packing-entomb a molecule in a slab of water. (I've had some rewarding chiselling erosion experiments with a simple text editor, by killing a range of TIP3's, and according CONECT entries). The only thing short of absolute bliss would be a salt script, which mutates a provided number of waters into, say, Na+Cl- pairs. Easy in perl, again. Well, this mail has certainly gotten much longer than I ever intended, while I have not yet covered everything. Anyway, what are your comments? Ideas? Flames? Thanks for listening so long, Regards, Eugene Leitl, MSU, Polym. Sci. Dept. P.S. To do some advertisement for perl/cgi-bin (which I can't dig yet, having bought 'Learning Perl' just few days ago): Here you can watch the (trivially simple) demo perl script in action: http://liposome.genebee.msu.su/cgi-bin/test If your MIME-aware web browser is correctly configured, it should spawn a pdb viewer (currently, I use RasMol, which can cope nicely even with the largest boxes supplied by Helmut) upon visiting the url. While the example is certainly silly, modifying it to make perl spit out dynamically generated pdb appears doable, and worthwhile. The trivially simple perl script (put the thing at below into your local cgi-bin, and fiddle with it): ftp://liposome.genebee.msu.su/pub/perl/test #!/usr/bin/perl -w # this Corina-generated pdb file should call RasMol, correct MIME conf. # provided print < Received: from SIUCVMB.SIU.EDU by SIUCVMB.SIU.EDU (IBM VM SMTP V2R2) with BSMTP id 5662; Thu, 22 Jan 98 10:41:31 CST Date: Thu, 22 Jan 98 10:36:56 CST From: "Tapas Kar, Ph.D, Asst. Scientist" To: chemistry@ccl.net Subject: Problem with excited state caln. with MOLCAS I am interested to calculate the S1/T1 states of Malonaldehyde. But I got some problem to get a pure S1 state. I had to take an average of two states. The input and part of the RASSCF output are enclosed. In this particular input I took the 50-50 average. An average of 10-90 or 90-10 does not lead to a pure S1 state. By pure S1 state I mean, the weight of the configuration 17 of root 2 should be greater than 0.9. And alaways I am getting a value in the range of 0.72 - 0.77. configuration 17 coefficient .872244 weight .760810 ( 3:1: 2: 2) symmetry 1 1 2 2 2 2 2 occupation 2 0 2 1 1 0 0 spin-coupling 3 0 3 1 2 0 0 Natural orbitals and occupation numbers for root 2 Occupation numbers for symmetry 1 1.971424 .028050 Occupation numbers for symmetry 2 1.932725 1.375825 .629482 .054140 .008354 values in 2nd and 3rd col. of symmetry 2 should be arround 1.0 instead of 1.37 and 0.63. Please suggest me how I can improve the result. Thanks for your attention and cooperation, Tapas Kar Rasscf Input file &RASSCF &END Title Malonaldehyde pt2 Iterations 50 50 LEVSHFT 0.0 Nactel 6 0 0 Inactive 15 1 Ras2 2 5 symmetry 1 Spin 1 CIRoot 2 2 1 2 1 1 LumOrb End of input Rasscf Output******* Convergence after 27 iterations 28 2 4 0 -265.21293103 -.18E-09 16 34 1 -.11E-05 .31E-04 .00 1.22 QN YES .05 .00 wave function printout: Split Graph format in parenthesis: midvertex, upper-walk symmetry, upper and lower-walk serial numbers ************************************************************************************************************************ printout of CI-coefficients larger than .05 for root 1 energy= -265.309683 configuration 16 coefficient .898219 weight .806796 ( 3:1: 1: 2) symmetry 1 1 2 2 2 2 2 occupation 2 0 2 2 0 0 0 spin-coupling 3 0 3 3 0 0 0 configuration 17 coefficient -.321184 weight .103159 ( 3:1: 2: 2) symmetry 1 1 2 2 2 2 2 occupation 2 0 2 1 1 0 0 spin-coupling 3 0 3 1 2 0 0 configuration 18 coefficient -.087996 weight .007743 ( 3:1: 3: 2) symmetry 1 1 2 2 2 2 2 occupation 2 0 2 0 2 0 0 spin-coupling 3 0 3 0 3 0 0 configuration 19 coefficient .123153 weight .015167 ( 3:1: 4: 2) symmetry 1 1 2 2 2 2 2 occupation 2 0 2 1 0 1 0 spin-coupling 3 0 3 1 0 2 0 printout of CI-coefficients larger than .05 for root 2 energy= -265.116179 configuration 16 coefficient .350120 weight .122584 ( 3:1: 1: 2) symmetry 1 1 2 2 2 2 2 occupation 2 0 2 2 0 0 0 spin-coupling 3 0 3 3 0 0 0 configuration 17 coefficient .872244 weight .760810 ( 3:1: 2: 2) symmetry 1 1 2 2 2 2 2 occupation 2 0 2 1 1 0 0 spin-coupling 3 0 3 1 2 0 0 configuration 18 coefficient -.059916 weight .003590 ( 3:1: 3: 2) symmetry 1 1 2 2 2 2 2 occupation 2 0 2 0 2 0 0 spin-coupling 3 0 3 0 3 0 0 configuration 20 coefficient -.168264 weight .028313 ( 3:1: 5: 2) symmetry 1 1 2 2 2 2 2 occupation 2 0 2 0 1 1 0 spin-coupling 3 0 3 0 1 2 0 Natural orbitals and occupation numbers for root 1 Occupation numbers for symmetry 1 1.978993 .020544 Occupation numbers for symmetry 2 1.944668 1.904601 .094931 .052511 .003753 Natural orbitals and occupation numbers for root 2 Occupation numbers for symmetry 1 1.971424 .028050 Occupation numbers for symmetry 2 1.932725 1.375825 .629482 .054140 .008354 Wave function specifications: ----------------------------- Number of closed shell electrons 32 Number of electrons in active shells 6 Max number of holes in RAS1 space 0 Max number of electrons in RAS3 space 0 Number of inactive orbitals 16 Number of active orbitals 7 Number of secondary orbitals 30 Spin quantum number .0 State symmetry 1 Orbital specifications: ----------------------- Symmetry species 1 2 Frozen orbitals 0 0 Inactive orbitals 15 1 Active orbitals 2 5 RAS1 orbitals 0 0 RAS2 orbitals 2 5 RAS3 orbitals 0 0 Secondary orbitals 26 4 Deleted orbitals 0 0 Number of basis functions 43 10 CI expansion specifications: ---------------------------- Number of configuration state fnc. 260 Number of determinants 625 Number of root(s) required 2 CI roots used 1 2 weights .5000 .5000 highest root include in the CI 2 Final optimization conditions: ------------------------------ Average CI energy -265.21293103 RASSCF energy -265.21293103 Super-CI energy .00000000 RASSCF energy change .00000000 Max change in MO coefficients -.503E-04 Max non-diagonal density matrix elemen .312E-04 Maximum BLB matrix element -.111E-05 (orbital pair 16, 34 in symmetry 1) Final state energy(ies): ------------------------ root number 1 E = -265.30968309 a.u. root number 2 E = -265.11617898 a.u. From kbyun@tams.chem.buffalo.edu Fri Jan 23 17:16:59 1998 Received: from tams.chem.buffalo.edu for kbyun@tams.chem.buffalo.edu by www.ccl.net (8.8.3/950822.1) id RAA02079; Fri, 23 Jan 1998 17:00:59 -0500 (EST) Received: from localhost (kbyun@localhost) by tams.chem.buffalo.edu (8.8.5/8.8.3) with SMTP id RAA09731 for ; Fri, 23 Jan 1998 17:00:59 -0500 (EST) Date: Fri, 23 Jan 1998 17:00:59 -0500 (EST) From: Kate Kyoungrim Byun To: chemistry@www.ccl.net Subject: Conversion of a file from charmm format to archive Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, everyone, I am trying to display an trajectory animation of an enzyme from charmm simulation, using insightII. The trajectory file obtained from charmm is a charmm formatted file and the file needed for insightII animation is an archive file. Here, I have a question. Is there any way to convert a charmm formatted file to an archive file which I can use for the insightII animation? Any suggestion will be appreciated. Thanks a lot for your time. Kate Byun From wjs@csb0.IPC.PKU.EDU.CN Fri Jan 23 22:17:01 1998 Received: from csb0.IPC.PKU.EDU.CN for wjs@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.8.3/950822.1) id WAA02946; Fri, 23 Jan 1998 22:01:56 -0500 (EST) Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA26425; Sat, 24 Jan 98 11:01:23 -0800 Date: Sat, 24 Jan 1998 11:01:23 -0800 (PST) From: Wang Jiansuo To: chemistry@www.ccl.net Subject: CROSSBOW(Computer Retrieval of Organic Substructures Based On Wiswesser) Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear listers: I am eager to look for a software named CROSSBOW(Computer Retrieval of Organic Substructures Based On Wiswesser).Any information is appreciated. Thanks. Sincerely yours,