From chatt@tniri.go.jp Fri Nov 24 00:37:17 1995 Received: from ripspost.aist.go.jp for chatt@tniri.go.jp by www.ccl.net (8.6.10/950822.1) id AAA13884; Fri, 24 Nov 1995 00:37:11 -0500 Received: from tnhost.tniri.go.jp by ripspost.aist.go.jp (8.6.9+2.4W/TISN-1.3/R2-AIST) id OAA21608; Fri, 24 Nov 1995 14:37:07 +0900 Received: by tnhost.tniri.go.jp (4.1/6.4J.6-tniri.MASTER) id AA06511; Fri, 24 Nov 95 14:36:28 JST Date: Fri, 24 Nov 95 14:36:28 JST From: chatt@tniri.go.jp (Abhijit Chatterjee) Message-Id: <9511240536.AA06511@tnhost.tniri.go.jp> To: chemistry@www.ccl.net Subject: Fe parameter I like to perform a MNDO calculation on Fe substituted molecule. I am using MOPAC 6.0., it does not have Fe parameter. Can anybody help me in getting the parameters of the same? A. Chatterjee chatt@tniri.go.jp TNIRI, AIST 4-2-1 NIGATAKE Miyaginoku, Sendai 983, JApan From owner-chemistry@ccl.net Wed Nov 22 13:06:48 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id MAA19468; Wed, 22 Nov 1995 12:59:22 -0500 Received: from xray5.chem.louisville.edu for dew01@xray5.chem.louisville.edu by bedrock.ccl.net (8.7.1/950822.1) id MAA21440; Wed, 22 Nov 1995 12:59:18 -0500 (EST) Received: by xray5.chem.louisville.edu (940816.SGI.8.6.9/930416.SGI) id MAA21987; Wed, 22 Nov 1995 12:59:17 -0500 From: dew01@xray5.chem.louisville.edu (D. E. Williams) Message-Id: <199511221759.MAA21987@xray5.chem.louisville.edu> Subject: New molecular packing software To: chemistry@ccl.net Date: Wed, 22 Nov 1995 12:59:16 -0500 (EST) Cc: dew01@xray5.chem.louisville.edu (D. E. Williams) Mpa/mpg is a new suite of programs designed for molecular packing analysis and molecular packing graphics in the unix environment. The capability of the mpa module extends from minimization of the energy of association of two or more molecules (e.g., molecular clusters and host-substrate docking) to energy minimization of a molecular assembly in a crystal lattice of any space group symmetry (e.g., crystal polymorph prediction). The software is capable of predicting space groups and reduced cells in which a given molecule may crystallize. Provision for limited molecular flexibility is made through selected rotations about intramolecular bonds. Molecular and/or crystal symmetry restrictions may be selectively applied as desired. A library of commonly available intermolecular force fields is included (e.g., WH86, MM85, Biosym, Charmm, Dreiding, etc.), and provision is made for user supplied force fields. The program selects energy minimization by OREM (off-ridge eigenvector minimization), SD (steepest descents), or NR (Newton-Raphson) as appropriate for the model. All first and second derivatives of the energy are calculated analytically; the second derivative matrix (hessian) is diagonalized and its eigenvectors determined. Simulated annealing is included to aid in locating global, rather than subsidiary, energy minima. The molecular packing graphics (mpg) module is closely integrated with the molecular packing analysis module to give users fast, convenient, and useful graphical visualization of the results. To obtain an abstract of the program and a listing of example calculations, send an email request to dew01@xray5.chem.louisville.edu. From szilagyi@indy.mars.vein.hu Wed Nov 22 07:06:43 1995 Received: from indy.mars.vein.hu for szilagyi@indy.mars.vein.hu by www.ccl.net (8.6.10/950822.1) id GAA12941; Wed, 22 Nov 1995 06:57:20 -0500 Received: by indy.mars.vein.hu (940816.SGI.8.6.9/930416.SGI.AUTO) id LAA07486; Wed, 22 Nov 1995 11:56:59 -0800 From: "Robert K. Szilagyi" Message-Id: <9511221156.ZM7484@indy.mars.vein.hu> Date: Wed, 22 Nov 1995 11:56:42 -0800 In-Reply-To: vkitzing@sunny.mpimf-heidelberg.mpg.de (Eberhard von Kitzing) "CCL:Molecular Mechanics" (Nov 22, 8:38am) References: <9511220738.AA00888@sunny.mpimf-Heidelberg.mpg.de> X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Re: CCL:Molecular Mechanics Cc: vkitzing@sunny.mpimf-heidelberg.mpg.de (Eberhard von Kitzing) > > The reason that I ask is that I obtained the following energies from > > MM optimisations for complexes of the same ligand but with different > > ions: My 0.02$ to this question is that molecular mechanical results MUST NOT be compared with each other if the molecules are different. It has no chemical and physical meaning at all! The MM model is constructed with different equations due to the different parameters. The different molecules contain different atom types, different bond types, thus represent different "sub force fields". Only when the non-valence type interactions are compared (van der Waals, Coulomb, etc.) can be acceptable in some cases and with heavy restrictions. I have successfully overcame this problem several times in case of transition metal complexes using a higher level of theory (semi-empirical or ab initio calculations) single point energy calculation. The absolute values of energies are still uncorrect, but realive values seem to be fine! Try it and let us know the results! Best wishes, Rob -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Robert K. Szilagyi University of Veszprem METMOD FF Ph.D. student Dept. Org. Chem. L1 Email: szilagyi@elod.vein.hu Veszprem, H-8201 L2 | R1 Phone: +36-(88)-422022/395 Egyetem u. 10 >W=C< :-) -> +36-(20)-461413 (0-24 h) P.O.Box 158 L3 | R2 FAX: +36-(88)-426016 HUNGARY L4 http://mm1.vein.hu/ http://mm2.vein.hu/~isom ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ *************** All opinions are my own, NOT my employer's *************** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From HGHSAM01@psipsy.uct.ac.za Tue Nov 21 09:06:29 1995 Received: from uctmail2.uct.ac.za for HGHSAM01@psipsy.uct.ac.za by www.ccl.net (8.6.10/950822.1) id IAA21125; Tue, 21 Nov 1995 08:57:39 -0500 Received: by uctmail2.uct.ac.za (Smail3.1.29.1 #14) id m0tHtC1-0004zdC; Tue, 21 Nov 95 15:57 SAT Message-Id: Received: by uctmail2.uct.ac.za (Mort 2.0a) id 12232 from PSIPSY; Tue Nov 21 15:57:01 1995 From: "sam" To: CHEMISTRY@www.ccl.net Date: Tue, 21 Nov 1995 16:00:55 SAST-2 Subject: Dendrimer modelling query Priority: normal X-mailer: Pegasus Mail v3.22 Hello all I am trying to find out what sort of modelling/computations have been done on dendrimers. I have searched through the CCL archives and contacted people who have previously done some work in this area. I would like to hear from anyone else out there who has done any modelling of dendrimers, to find out what exactly has been done and what sort of properties were studied. Thanks for your time Samantha ********************************************************************** Samantha Hughes HGHSAM01@psipsy.uct.ac.za Department of Chemistry University of Cape Town ********************************************************************** From smori@chem.s.u-tokyo.ac.jp Tue Nov 21 19:06:33 1995 Received: from utsc.s.u-tokyo.ac.jp for smori@chem.s.u-tokyo.ac.jp by www.ccl.net (8.6.10/950822.1) id SAA03710; Tue, 21 Nov 1995 18:54:03 -0500 Received: from [133.11.6.112] (smori.chem.s.u-tokyo.ac.jp) by utsc.s.u-tokyo.ac.jp (5.67+1.6W/TISN-1.3/R2) id AA23160; Wed, 22 Nov 95 08:48:24 JST Message-Id: <9511212348.AA23160@utsc.s.u-tokyo.ac.jp> Date: Wed, 22 Nov 1995 08:57:56 +0900 To: chemistry@www.ccl.net From: smori@chem.s.u-tokyo.ac.jp (Mori Seiji) X-Sender: smori@chem.s.u-tokyo.ac.jp (Unverified) Subject: NMR shift and coupling constant calculation Cc: smori@utsc.s.u-tokyo.ac.jp Dear everybody, Recently, many letters about NMR chemical shift calculation were posted, and I am also interested in NMR shifts in organic and organometallic complexes in solution. I have several questions, 1. How is the reliablities of 1.1 methods (GIAO, IGAIM, CSGT, IGLO) 1.2 theory (HF,DFT,MP2...CC) and basis-sets 1.3 How is the solvent effect of polarity on the NMR shift, coupling constant (I think it is not related calcluation , probably it is a fundamental question about NMR)? 2. Do you know the program or references which one can calculate not only chemical shift but also the coupling constant ( for example, 1H-1H and 13C-13C) and NOE in quantum chemistry other than G94? As to 1H-1H coupling constant, many programs such as PCMODEL was supported but its calculation is not QC. If you have comments and indicate the references, would you please send me ? I will summarize replies. Thanks in advance, Seiji Mori #################################################### Seiji Mori Graduate student in Nakamura Laboratory Department of Chemistry The University of Tokyo Hongo 7-3-1, Bunkyou-ku, Tokyo 113, JAPAN email:smori@chem.s.u-tokyo.ac.jp #################################################### From peon@medchem.dfh.dk Fri Nov 24 04:52:20 1995 Received: from danpost.uni-c.dk for peon@medchem.dfh.dk by www.ccl.net (8.6.10/950822.1) id EAA17145; Fri, 24 Nov 1995 04:41:54 -0500 Received: from medchem.dfh.dk (medchem.dfh.dk [130.225.177.15]) by danpost.uni-c.dk (8.6.4/8.6) with ESMTP id KAA11899; Fri, 24 Nov 1995 10:41:46 +0100 Received: from [130.225.177.59] by medchem.dfh.dk via SMTP (940816.SGI.8.6.9/940406.SGI) id LAA13460; Fri, 24 Nov 1995 11:03:00 +0100 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 24 Nov 1995 10:41:48 +0100 To: toukie@zui.unizh.ch From: peon@medchem.dfh.dk (Per-Ola Norrby) Subject: Re: CCL:Diameter of a globular peptide Cc: chemistry@www.ccl.net S. Shapiro wrote > I was recently asked what would be the approximate theoretical diameters >of globular peptides of molecuar weight 3,000 and 10,000. If anyone knows >how to calculate this, I would be grateful if you would share with me the >method of calculation. > Depends on how accurate you want to be. Assuming a perfect sphere with the density of water, molecular weight 10,000 corresponds to a diameter of approx. 32 A. If you want something more accurate, I'd say a simple empirical method would be to correlate the Mw of some known structures with r^3. Of course, you could spend a couple of thousand CPU hours on molecular dynamics runs and average.... Per-Ola Norrby ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ --- Bureaucracy is a challenge to be conquered with a righteous attitude, a tolerance for stupidity, and a bulldozer when necessary -- Peter's Law 15. * Per-Ola Norrby * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * tel. +45-35376777-506, +45-35370850 fax +45-35372209 * Internet: peon@medchem.dfh.dk, peo@compchem.dfh.dk From tamasgunda@tigris.klte.hu Fri Nov 24 06:07:21 1995 Received: from tigris.klte.hu for tamasgunda@tigris.klte.hu by www.ccl.net (8.6.10/950822.1) id FAA17726; Fri, 24 Nov 1995 05:54:16 -0500 Message-Id: <199511241054.FAA17726@www.ccl.net> Received: from anti02 (anti02.chem.klte.hu) by tigris.klte.hu (MX V4.1 VAX) with SMTP; Fri, 24 Nov 1995 11:56:33 EST Sender: X-MX-Warning: Warning -- Invalid "From" header. From: "tamasgunda@tigris.klte.hu" To: chemistry@www.ccl.net Date: Fri, 24 Nov 1995 11:56:29 +1 Subject: Re: CCL:Convert 3D structure to 2D Priority: normal X-mailer: Pegasus Mail/Windows (v1.22) Hi netters, Arthur Wang wrote: > Are there any softwares whcih can convert 3D structures of small organic > compounds from, say, MOL2 or PDB format to comfortable 2D topological > structures? > > It is not a strange question. Maybe you will like to show a structure > derived from molecular modeling software on a piece of paper. In this > case, projection of the 3D structure does not work because it is not in > the favor of organic chemists. You can draw it by yourself but when there > are dozens of structures, it becomes a disturbing job. > > Any ideas? Thanks in advance. > I think the problem is the same as in the case of another quite often heard question: is there any program to convert a SMILES string back to graphical structure? Generally, how to draw/restore the structure >from pure connectivity information, and in turn, the result should please the eyes of organic chemists. There are some programs, but as a whole, I am quite pessimistic. It can be done easily in the case of aniline or dodecylbromide, but how about a complicated natural product like taxol or strychnine or a cyclopeptide or a macrolid antibiotics? It is nearly impossible to create an algorithm which could figure out what kind of projection is the "desired" one. Maybe a program with an immense structural library could solve the majority of the cases. So I would be also glad to hear about such a program. Best wishes Tamas ************************************************************************ Tamas E. Gunda, Ph.D. phone: (+36-52) 316666 ext 2479 Research Group of Antibiotics fax : (+36-52) 310936 L. Kossuth University e-mail: tamasgunda@tigris.klte.hu POBox 36 H-4010 Debrecen Hungary ************************************************************************ From vkitzing@sunny.mpimf-heidelberg.mpg.de Fri Nov 24 08:37:23 1995 Received: from otto.mpimf-heidelberg.mpg.de for vkitzing@sunny.mpimf-heidelberg.mpg.de by www.ccl.net (8.6.10/950822.1) id IAA19078; Fri, 24 Nov 1995 08:22:16 -0500 Received: from [192.109.43.34] (mac10.mpimf-heidelberg.mpg.de) by otto.mpimf-heidelberg.mpg.de (4.1/SMI-4.1) id AA16886; Fri, 24 Nov 95 14:20:45 +0100 Date: Fri, 24 Nov 95 14:20:45 +0100 Message-Id: <9511241320.AA16886@otto.mpimf-heidelberg.mpg.de> To: toukie@zui.unizh.ch From: vkitzing@sunny.mpimf-heidelberg.mpg.de (Eberhard von Kitzing) Subject: Re: CCL:Two questions Cc: CHEMISTRY@www.ccl.net (Computational Chemistry List) Dear Prof. Shapiro, > (ii) Does anyone have any information on experimental (preferred) > or theoretical (OK) values for the dielectric constant in > the interior of lipid bilayers, artificial membranes, or > (preferred) biological membranes? There is no simple answer to this question. In the experimental as well as in the theoretical case the answer depends on what property you are concentrating. Membranes, especially biological ones, are highly inhomogeneous. Thismeans that the local dielectric constant does vary from place to place (perhaps in the range between 2.5 for hydrocarbones to 6 for more polarizable materials). The situation get more complicated if you consider the effective dielectric constant, a measure of the screening of two charges due to the presence of the dielectric properties of water and the membrane. In this case, the value cannot be lower than the membrane dielectric constant but can become large than the water dielectric constant. This problem has been considered for estimating the energy barriers for ions permeating through ion channels. For this problem there exists a huge amount of literature (see below). In these studies, however, the effect of the electrolyte has often been neglected. Counter ions always increase the charge-charge screening. %0 Journal Article %A Parsegian, V. Adrian %D 1969 %T Energy of an Ion crossing a Low Dielectric Membrane: Solutions to Four Relevant Electrostatic Problems %J Nature %V 221 %P 844-846 %K continuum theory, dielectric constant, membrane, ion channels, ion carriers, mirror image, image charge, image force %X The influences on ion energy of membrane thickness, ion-pair formation, pores, and carriers have been estimated. Only pores and carriers lower the energy barrier significantly %0 Journal Article %A Parsegian, V. Adrian %D 1975 %T Ion-Membrane interactions a structural forces %J Annals of the New York Academy of Sciences %V 264 %P 161-174 %K continuum theory, dielectric constant, membrane, ion channels, ion carriers, mirror image, image charge, image force %0 Book Section %A Jordan, Peter C. %D 1993 %T Interactions of ions with membrane proteins %B Thermodynamics of Membrane Receptors and Channels %E Jackson, Meyer B. %I CRC Press %C Boca Raton %P 27-80 %K continuum model, effective dielectric constant, Born energy, Eyring theory, Nernst-Planck equation, energy profiles, gramicidine, ionic strength effects, conductivity, alamethicin, acetylcholin receptor channel, voltage gated channels, anion channels %0 Journal Article %A Partenskii, Michael B. %A Dorman, Vladimir %A Jordan, Peter C. %D 1994 %T Influence of a channel-forming peptide on energy barriers to ion permeation, viewed from a continuum dielectric perspective %J Biophysical Journal %V 67 %N 4 %P 1429-1438 %K ** gramicidin channel; dynamics; water; model; electrostatics; simulations; movement; constant; membrane electrostatic barrier; electrostatic screening; ion transport; ionic conductivity; dielectric screening %0 Journal Article %A Zhou, F. %A Schulten, K. %D 1995 %T Molecular-dynamics study of a membrane water interface %J Journal of Physical Chemistry %V 99 %N 7 %P 2194-2207 %F Review %K ** lipid bilayer-membranes; hydration forces; phospholipid-bilayers; computer-simulation; dilauroylphosphatidylethanolamine bilayers; electrostatic interactions; amphiphilic surfaces; dielectric-constant; boundary-conditions; magnetic-resonance; ------------------------------------------------------------------------- Eberhard von Kitzing Max-Planck-Institut fuer Medizinische Forschung Jahnstr. 29, D69120 Heidelberg, FRG Carl-Zuckmayer Str. 17, D69126 Heidelberg (privat) FAX : +49-6221-486 459 (work) Tel.: +49-6221-486 467 (work) Tel.: +49-6221-385 129 (home) internet: vkitzing@sunny.MPImF-Heidelberg.mpg.de http://sunny.mpimf-heidelberg.mpg.de/people/vkitzing/Eberhard.html From fgonzale@lauca.usach.cl Fri Nov 24 10:37:25 1995 Received: from ralun.usach.cl for fgonzale@lauca.usach.cl by www.ccl.net (8.6.10/950822.1) id KAA20352; Fri, 24 Nov 1995 10:29:30 -0500 Received: from lauca.usach.cl (lauca.usach.cl [158.170.64.28]) by ralun.usach.cl (8.6.11/8.6.9) with ESMTP id LAA09249 for ; Fri, 24 Nov 1995 11:30:04 -0600 Received: (from fgonzale@localhost) by lauca.usach.cl (8.6.12/8.6.12) id MAA23888 for chemistry@www.ccl.net; Fri, 24 Nov 1995 12:29:10 -0300 From: Fdo Danilo Gonzalez Nilo Message-Id: <199511241529.MAA23888@lauca.usach.cl> Subject: about ZINDO To: chemistry@www.ccl.net Date: Fri, 24 Nov 95 12:29:09 ADT Hi All! anybody has any comment or refence about the use of ZINDO for polymer calculation (polypyrrole, polyaniline, etc). Also about any comparison with AM1, PM3, EHT, etc. I'm wating for yours respond!! thank! Fernando Danilo Gonzalez N. Facultad de Quimica y Biologia Universidad de Santiago de Chile E-mail : fgonzale@lauca.usach.cl From cletner@remcure.bmb.wright.edu Fri Nov 24 10:52:25 1995 Received: from remcure.bmb.wright.edu for cletner@remcure.bmb.wright.edu by www.ccl.net (8.6.10/950822.1) id KAA20582; Fri, 24 Nov 1995 10:47:55 -0500 Received: by remcure.bmb.wright.edu (931110.SGI/921111.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA26686; Fri, 24 Nov 95 13:39:55 -0500 Date: Fri, 24 Nov 1995 13:39:49 -0500 (EST) From: Charles Letner To: "Robert K. Szilagyi" Cc: CHEMISTRY@www.ccl.net, Eberhard von Kitzing Subject: Re: CCL:Re: CCL:Molecular Mechanics In-Reply-To: <9511221156.ZM7484@indy.mars.vein.hu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 22 Nov 1995, Robert K. Szilagyi wrote: > My 0.02$ to this question is that molecular mechanical results MUST NOT > be compared with each other if the molecules are different. It has no chemical > and physical meaning at all! The MM model is constructed with different > equations due to the different parameters. So the question that I always end up at is, what constitutes a different molecule? Further, how to assess whether two molecules are "close enought." For example, a organic molecule may have a chiral center. So what about the two conformers? I would say they are close enough to compare energies. However, it is not diffiult to envison a case in which the non-bonded interactions between the two are not the same. As a consequence, the two have different "equations." For the biopolymer case, how about two calculations in which different amounts of solvent are added? Though the biopolymer may be identical in the two systems the solvent will be different. In this case the energy of the system will be different. As a result, I expect that the energy of the biopolymer will be different. I quess then the question of MD calculations to estimate free energy differences then begs to be asked - but I'll stay away from that..... ;) My $0.02 worth. Chuck Charles Letner Wright State University Department of Biochemistry Dayton, OH 45435 e-mail: cletner@remcure.bmb.wright.edu From quchunxu@bio.titech.ac.jp Fri Nov 24 03:40:55 1995 Received: from titbio-gw.bio.titech.ac.jp for quchunxu@bio.titech.ac.jp by www.ccl.net (8.6.10/950822.1) id DAA16650; Fri, 24 Nov 1995 03:38:37 -0500 Received: by titbio-gw.bio.titech.ac.jp (5.67+1.6W/tit-mx1.1); Fri, 24 Nov 95 17:34:00 JST Date: Fri, 24 Nov 95 17:34:00 JST From: Qu Chunxu Message-Id: <9511240834.AA09126@titbio-gw.bio.titech.ac.jp> To: calculation@bio.titech.ac.jp, cavity@bio.titech.ac.jp, chemistry@www.ccl.net, of@bio.titech.ac.jp Subject: Summary: Cavities in Proteins || WARNING!!! This message was heavily edited by the list administrator || to edit out headers/footers/signatures/duplicates/etc. The original message || was over 50kB long, and the distribution software rejected it as too large. || Sorry if I had to delete your witty signatures impressive paths in your || headers and detailed information about the e-mail software you are using Dear netter, Several days ago I posted a question at this list, and I got some methods to solve my problem. Here I want to express my sincerest thanks to all of you who pay attention to my problem. The following is the summary of the answers I received: PROBLEM: >Dear netters, > >I met a problem on cavity volume calculation. > >I am studying on the thermostability of 3-isopropylmalate dehydrogenase. >Protein engineering showed that at a certain site, Ala-->Leu mutation >increased the stability of protein. Crystallography analysis showed that the >sidechain of Leucine reduced the cavity around mutation site. Although the >dot surface illustration can show this point very well, we are asked to give >the cavity volume in each case. However, we have no such a program. Could you >help me? Thanks in advance. ANSWERS: 1) summary from eldbjorg@chem.uit.no I asked a more generally question concerning cavities in this forum - I am using "GRASP" to find the cavities and give the area or volume of these cavities. If the program does not find a cavity around the mutation site. then I am not sure how you could quantify (volum/area) it. Anyway: here are the answers to my question: =================================== From: Volkhard.Helms@EMBL-Heidelberg.de (Volkhard Helms) Date: Tue, 31 Oct 1995 12:25:14 +0100 Hello, the 'standard' way is to role a solvent probe over the protein surface. Different probe radius are being used (1.25A - 1.4A). The GRASP program has a very easy to use implementation that spits out the volume of the cavities and displays a molecular surface of the cavities. You might be interested in the following two papers: Williams et al. Protein science, 3, 1224-1235 (1994) and Hubbard et al. Protein engineering, 7, 613-626 (1994) that deal with protein cavities. Hope this helps, Volkhard -- Volkhard Helms European Molecular Biology Laboratory Meyerhofstr.1 69012 Heidelberg, Germany Tel. +49 - 6221 - 387255 e-mail: helms@embl-heidelberg.de ================================================ From: Leif Laaksonen Subject: Re: CCL:Cavities within proteins Hi, You should be able to calculate them in much the same way as we did it for cavities in polyisobutylene (PIB): http://www.csc.fi/lul/chem/movies/pib/pib_movies.html Regards, -leif laaksonen ------------------------------------------------------------------- Leif Laaksonen | Center for Scientific Computing | Phone: 358 0 4572378 P.O. Box 405 | Mobile: 358 400425203 FIN-02101 Espoo | Telefax: 358 0 4572302 FINLAND | Mail: Leif.Laaksonen@csc.fi ---------URL: http://laaksonen.csc.fi/leif.laaksonen.html---------- ====================================== From: hauer@ftdetrck-ccmail.army.mil Subject: Finding and filling protein cavities. J Mol Graph Is this what you're looking for? [Sometimes I'm way off on interpreting the question.] ---------------------------------------------------------------- 1 AU - Delaney JS TI - Finding and filling protein cavities using cellular logic operations MH - Proteins MH - Methods MH - docking MH - Protein Binding MH - Binding Sites MH - Cytochrome P 450 MH - Logic MH - Models,Molecular MH - Pattern Recognition MH - Protein Conformation MH - Software AB - A method for solid-filling protein cavities is presented. The method uses a pattern-recognition technique based on cellular logic operations to distinguish between convex and concave regions of a protein. In doing this it solid fills protein cavities and automatically defines a boundary between cavity and exterior free space. The operations used to fill the cavities also can be used to process the filler to filter out small-scale features. So far the main use of the method has been in --> visualizing protein active sites for docking. The method can be --> used to find cavities of a given size range and could be used to find novel protein binding sites SO - J Mol Graph 1992;10:174-7 Ed --------------------------------------------------------------------------- Edward C. Hauer /\ Dept Cell Biol Biochem GOOD / \ FAST Toxinology Division, USAMRIID / \ Ft. Detrick, MD 21602-5011 USA / Pick Two \ 301 619-4813 619-2348 fax /________________\ hauer@ftdetrck-ccmail.army.mil CHEAP ==================================================================== From: gareth Subject: Re: CCL:Cavities within proteins Have a look at: Cavity search: an algotithm for the isolation and display of cavity-like binding regions. Ho & Marshall JCAMD 4 (1990) 337-354 and Finding and filling protein cavities using cellular logic operations. Delaney JMolGraph 10 (1992) 174-177 Gareth. -- Gareth Jones Dept of Information Studies and Krebs Institute for Biomolecular Research University of Sheffield, UK E-mail gareth.jones@sheffield.ac.uk ================================================================== From: waller@thor.herl.epa.gov (Dr. Chris L. Waller) Subject: Re: CCL:Cavities within proteins Status: R > Chris M.W. Ho and Garland R. Marshall have a program named appropriately CAVITY. Contact Center for Molecular Design, Washington University, St. Louis, MO. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Chris L. Waller, Ph.D. Modeling Team Leader / Research Chemist Pharmacokinetics Branch (MD-74) Experimental Toxicology Division National Health and Environmental Effects Research Laboratory U.S. Environmental Protection Agency Research Triangle Park, NC 27711 (919) 541-7976 (office) (919) 541-0704 (lab) (919) 541-5394 (fax) waller@thor.herl.epa.gov %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ========================================================================== From: Vincent Collura Subject: Re: CCL:Cavities within proteins There is an article in Protein Engineering (1994 or 1995) from Patrick Argos et al. Cheers Vincent. ========================================================================= From: Roman Laskowski Subject: Cavities in proteins Dear Eldbjoerg, A colleague of mine here at University College London has passed me your enquiry about calculating cavities in proteins. I have a program called SURFNET which does just that. The paper describing it should appear in the next issue of J.Mol.Graphics, but you can find out about the program, and how to get a copy, via the following URL: http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html Cavities and surface clefts are computed as "gap regions" between atoms of the protein. Alternatively, you can compute gaps between two molecules, such as the separate chains of a dimer, or the gaps between a protein and its ligand. The program's output can be viewed on a number of molecular modelling packages used for displaying proteins, such as Quanta, O, Sybyl and Insight. The source code (in FORTRAN) is free to academic users. All you need to do is sign and return a Confidentiality Agreement. There are several other programs that compute cavities. Below I give the LaTeX version of an extract from my SURFNET paper mentioning the other programs and giving references. I hope this helps. Best wishes, Roman Laskowski. ------------------------------------------------------------------------ A number of programs are available for visualizing molecular surfaces and cavities. Molecular surfaces are most usually displayed as dot-surfaces$^{\cite{Connolly 1983}}$ by the commonly-used molecular modelling programs, such as {\em O}$^{\cite{Jones et al 1991}}$ and {\sc quanta}$^{TM}$ (Molecular Simulations Inc., Burlington, MA, USA). The dots are placed at the van der Waals radius of each atom, at a given density and colouring, and provide an indication of the molecular surface. Where two molecules interact, their dot-surfaces can show their complementarity at the interface. Solid renderings of surfaces can also be generated by these and other packages (ref. \cite{Zauhar 1995} and references therein), with appropriate texturing and reflections$^{\cite{Connolly 1993}}$. For large molecules, such as proteins, these representations are difficult to manipulate interactively on the graphics, although graphics packages exist that can do this well, such as {\sc avs} (Advanced Visual Systems Inc., Waltham, MA, USA). One excellent program designed specifically for visualizing molecular surfaces, and in particular their electrostatic potentials, is {\sc grasp}$^{\cite{Nicholls et al 1993}}$ which has quickly become very popular because of the striking images it generates. Various methods and programs exist for visualizing cavities and surface grooves. Both types of region are difficult to perceive from just viewing a molecular surface alone. A given cavity, as defined by the convex surface of the atoms surrounding it, is a concave region which, because the atoms cannot fit together without leaving gaps, branches into myriads of channels and grooves in all directions and is impossible for the mind to grasp. Programs that best depict cavities, therefore, show them as convex surfaces, often built up by fitting probe spheres into the cavities in some manner, and then defining a surface around the resultant collection of inter-penetrating spheres. By defining a minimum sphere size, the myriads of small gaps and crevices between the atoms are excluded and only the significant gaps are depicted. Internal cavities, which are completely closed off from the outside world, are relatively easy to detect. The program of Ho \& Marshall$^{\cite{Ho & Marshall 1990}}$, for example, `flood-fills' a cavity from a given start point. The {\sc voidoo} program$^{\cite{Kleywegt & Jones 1994}}$ detects cavities, and certain invaginations as well, by an `atom-fattening' procedure which progressively closes off small channels both between cavities and also between cavities and the outside world by gradually increasing the atomic radii. The {\sc hole} program of Smart {\em et al.}$^{\cite{Smart et al 1993}}$ is specifically geared to identifying, measuring and visualizing ion channels in proteins, stepping through the channel from a given start-point and filling it with spheres. Some programs locate internal cavities as a by-product of generating the molecular surface. For example, the {\sc grasp} program, mentioned above, locates internal cavities on the basis of the connectivities of the surface elements. Similarly, the algorithm of Voorintholt {\em et al.}$^{\cite{Voorintholt et al 1989}}$, which is used by the {\sc what if} molecular modelling package$^{\cite{Vriend 1990}}$, can show the molecular surface that is accessible to different probe sizes as a density map, and so can detect the molecule's internal cavities. Surface grooves and indentations, on the other hand, are much more difficult to depict - principally because of the difficulty of knowing how far into open space to extend the groove region; where does the `sea level' of that part of the surface lie? The program of Delaney$^{\cite{Delaney 1992}}$ uses a pattern recognition technique to identify the limits for the flood-filling procedure. The {\sc pocket} program$^{\cite{Levitt & Banaszak 1992}}$ is an interactive cavity-filling program which detects pocket regions in the structure by placing trial a sphere of a given radius at points on a 3D grid. At each grid-point the sphere either makes, or does not make, contact with atoms from the molecule. Regions of no contact which are bounded by contact regions in either the $x$-, $y$- or $z$- directions are deemed to be cavities or pockets. Other cavity-detection algorithms concern themselves primarily with the detection and analysis of cavities rather than with their visualization (for example, refs \cite{Hubbard et al 1994}--\cite{Williams et al 1994}). These usually involve moving a probe sphere about the surface to detect completely or partially buried voids. References:- ---------- \bibitem{Connolly 1983} Connolly, M. L. Analytical molecular surface calculation. {\em J. Appl. Cryst.} 1983, {\bf 16}, 548--558 \bibitem{Jones et al 1991} Jones, T. A., Zou, J-Y., Cowan, S. W., and Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. {\em Acta Cryst.} 1991, {\bf A47}, 110--119 \bibitem{Zauhar 1995} Zauhar, R. J. SMART: a solvent-accessible triangulated surface generator for molecular graphics and boundary element applications. {\em J. Comput. Aided Mol. Des.} 1995, {\bf 9}, 149--159 \bibitem{Connolly 1993} Connolly, M. L. The molecular surface package. {\em J. Mol. Graph.} 1993, {\bf 11}, 139--141 \bibitem{Nicholls et al 1993} Nicholls, A., Bharadwaj, R., and Honig, B. GRASP: graphical representation and analysis of surface-properties. {\em Biophys. J.} 1993, {\bf 64}, A166 \bibitem{Ho & Marshall 1990} Ho, C. M. W., and Marshall, G. R. Cavity search: an algorithm for the isolation and display of cavity-like binding regions. {\em J. Comput. Aided Mol. Des.} 1990, {\bf 4}, 337--354 \bibitem{Kleywegt & Jones 1994} Kleywegt, G. J., and Jones, T. A. Detection, delineation, measurement and display of cavities in macromolecular structures. {\em Acta Cryst.} 1994, {\bf D50}, 178--185 \bibitem{Smart et al 1993} Smart, O. S., Goodfellow, J. M., and Wallace, B. A. The pore dimensions of gramicidin A. {\em Biophys. J.} 1993, {\bf 65}, 2455--2460 \bibitem{Voorintholt et al 1989} Voorintholt, R., Kosters, M. T., Vegter, G., Vriend, G., and Hol, W. G. J. A very fast program for visualizing protein surfaces, channels and cavities. {\em J. Mol. Graphics} 1989, {\bf 7}, 243--245 \bibitem{Vriend 1990} Vriend, G. WHAT IF: a molecular modeling and drug design program. {\em J. Mol. Graphics} 1990, {\bf 8}, 52--56 \bibitem{Delaney 1992} Delaney, J. S. Finding and filling protein cavities using cellular logic operations. {\em J. Mol. Graph.} 1992, {\bf 10}, 174--177 \bibitem{Levitt & Banaszak 1992} Levitt, D. G., and Banaszak, L. J. {\sc pocket}: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. {\em J. Mol. Graphics} 1992, {\bf 10}, 229--234 \bibitem{Rashin et al 1986} Rashin, A. A., Iofin, M., and Honig, B. Internal cavities and buried waters in globular proteins. {\em Biochemistry} 1986, {\bf 25}, 3619--3625 \bibitem{Alard & Wodak 1991} Alard, P., and Wodak, S. Detection of cavities in a set of interpenetrating spheres. {\em J. Comp. Chem.} 1991, {\bf 12}, 918--922 \bibitem{Williams et al 1994} Williams, M. A., Goodfellow, J. M., and Thornton, J. M. Buried waters and internal cavities in monomeric proteins. {\em Protein Sci.} 1994, {\bf 3}, 1224--1235 ======================================================================== From: David Clark Subject: CCL: cavities in Proteins Hello, Here is a reference that might be of interest: author = "Lewis, R.A. ", title = "Determination of Clefts in Receptor Structures ", journal = "Journal of Computer--Aided Molecular Design ", year = "1989 ", volume = "3 ", pages = "133--147 ", There was also a paper by Ho and Marshall back in 1992 or 1993 about a program called CavitySearch - it was in JCAMD, I think. Best wishes David Clark ., David E. Clark | Proteus Molecular Design Ltd., | Tel: 01625-500555 Lyme Green Business Park, | Fax: 01625-500666 Macclesfield, Cheshire, | Email: D.E.Clark@proteus.co.uk SK11 0JL, UK | =================================================================== From: stoutepf@carbon.dmpc.com (Pieter Stouten) Subject: Re: CCL:Cavities within proteins Check out WHATIF by Gert Vriend . Cheers, Pieter. ** Note that my e-mail address has changed once again. I hope it will not ** ** happen again soon. Please use stoutepf@carbon.dmpc.com from now on. ** Pieter Stouten || Nothing shocks me; Computer Aided Drug Design Group || The DuPont Merck Pharmaceutical Company || I am a scientist! P.O. Box 80500, Wilmington, DE 19880-0500 || Phone: +1 (302) 695 3515 || -- Fax: +1 (302) 695 2813 || Internet: stoutepf@carbon.dmpc.com || Indiana Jones ======================================================================== From: Craig Taverner Subject: Re: CCL:Cavities within proteins What do you mean by "calculate cavities"? Do you mean calculate the cavity volume? If so, I have a program I wrote to calculate the volume of cavities in crystals, but should work for proteins too if you already know where the cavity is. If you're interested the program is: ftp://hobbes.gh.wits.ac.za/pub/steric/steric_1.08.tgz It's original purpose was for cone and solid angle calculations, but it has since been substantially extended. Cheers, Craig "If God had meant us to be naked, we would have been born that way." Craig Taverner Structural Chemistry, University of the Witwatersrand, South Africa =================================================================== From: Scott Weston Subject: Re: CCL:Cavities within proteins Eldbjoerg, Depending on what your exact needs are, one good approach to the isolation and visualization of protein cavities is the one encoded in the CAVITY SEARCH program by Chris Ho and Garland Marshall at the Center for Molecular Design (J Comput Aided Mol Des (JCB), 1990 Dec; 4 (4): 337-54. More information is available at their Web site at http://wucmd.wustl.edu. Good luck, Scott Scott Weston Lab Phone: (601) 232-7187 Grad. Student Lab FAX: (601) 232-5118 Dept. of Medicinal Chemistry Home Phone: (601) 234-0067 University of Mississippi mcgsw@cotton.vislab.olemiss.edu University, MS 38677 ================================================================= From: marvin@biosym.com (Marvin Waldman) Subject: Finding cavities in proteins Hi Eldbjoerg, A nice algorithm for doing this can be found in the following reference: "Finding and filling protein cavities using cellular logic operations," John S. Delaney, J. Mol. Graphics, vol. 10, pp. 174-177 (1992). Regards, Marvin Waldman, Ph.D. Biosym/MSI e-mail: marvin@biosym.com ========================================================================= From: john delaney Subject: re: cavities in proteins Dear Eldbjorg, With regards to your query, I published a paper on the subject 3 years ago in the Journal of Molecular Graphics. Briefly, the program described finds cavities in proteins using a simple pattern recognition technique. The paper includes some references to similar work by other people. John S. Delaney, Finding and filling protein cavities using cellular logic operations, J. Mol. Graphics, 1992, Vol 10, pp 174-177 I can send a reprint if your interested. Hope this helps. John Delaney Zeneca Agrochemicals, Jealott's Hill Research Station, Bracknell, Berkshire, UK E-mail: delaney@jh01sg.demon.co.uk =============================================================== From: "Don Gregory" Subject: CCL:Protein Cavities Quanta/Protein users will recognize this as a capability in the Protein Health toolset. Don Gregory ================================================================= From: connolly@netcom.com (Michael L. Connolly) I've written some C software for identifying protein cavities. I license source code to universities for what I think is a modest fee. $300 (U.S.) for PQMS, which computes volumes & areas; $200 (U.S.) more for TRB, which converts PQMS output to SGI Inventor files Please take a look at my anonymous ftp site: ftp.netcom.com cd pub/co/connolly In particular, fetch my documentation in RTF format: cavity.rtf and sample output files in SGI Inventor and Image formats: lysozyme.iv lysozyme.rgb Please send me E-mail if you have any questions. Mike Michael L. Connolly connolly@netcom.com 1259 El Camino Real, #184 (415) 780-0321 (voice) Menlo Park, CA 94025 (415) 780-0321 (fax) United States of America (415) 326-4203 (fax) ------------------------------------------------------------------- 2) Program MSDOT(Connolly) from goeller@organik.uni-erlangen.de Just have a look at the QCPE bulletins. There are some programs like GEPOL, MSDOT (Conolly), one by Richards and some programs, which inhibit some of the secodes in one. Bye, AHG... Andreas Goeller Computer Chemie Centrum der Dipl.-Chem. Universitaet Erlangen/Nuernberg Naegelsbachstr. 25 phone: +49(0)9131-856583 D-91052 Erlangen fax: +49(0)9131-856565 Germany email: goeller@organik.uni-erlangen.de http://www.organik.uni-erlangen.de ----------------------------------------------------------------- 3) QUANTA/PROTEIN HEALTH/HOLES * from masayuki@hsc.usc.edu My colleague told me that the software QUANTA 4.0 from Molecular Simulations, Inc. (MSI) has a module for cavity volume calculations. You can call MSI at (03)3818-6511 in Japan. Sincerely, Masayuki Yuki University of Southern California School of Pharmacy masayuki@hsc.usc.edu ------------------------------------------------------------------- ** from mjf@biosym.com (Mark J Forster ) The Quanta/Protein Health software includes a tool for locating holes in a protein structure that are typically large enough to accomodate a water molecule. The method places the protein on a 3D grid and tags grid points as either protein or solvent depending upon their proximity to a protein atom.> Once the grid points for bulk solvent around the protein are identified by a flood fill technique then the non protein grid points that remain are possible solvent sized cavities within the protein. The minimum size of the hole detected may be set by the user. Hope this helps. Best Wishes __________________________________________________________ Mark / ___ / / /| / Mark J Forster / / | / Biosym / Molecular Simulations. /__/__|/ \__O_/ 9685 Scranton Rd, /__/ | San Diego, CA 92121, USA. / | /| Tel: (619) 458 9990 / o |<-------- / | FAX: (619) 458 0136 /__ __| e-mail: mjf@biosym.com ------------------------------------------------------------- 4) ftp://hobbes.gh.wits.ac.za/pub/steric/steric_1.08.tgz from craig@hobbes.gh.wits.ac.za I have a program to calculate various steric effects in molecules and crystals, and recently added a cavity volume calculation to it for the calculation of the cavity volume in the region of perchlorate groups in crystals. The main way of calculating the cavity volume is using a Monte Carlo sampling approach, which gives very fast results, with moderate accuracy. There are four different cavity volumes calculated, depending on exactly what is meant by cavity volume (depends mainly on how you define the boundry to the cavity). Unfortunately the program does not yet include a cavity search algorithm, so you have to tell it exactly where the cavity is. If you're interested, the program is available at: ftp://hobbes.gh.wits.ac.za/pub/steric/steric_1.08.tgz There is a readme file for installation info, and online help, but I'd recommend you e-mail me for specific info, particularly about the cavity volume calculation, because it's quite a new addition to the program. The program was developed under linux unix, but has been compiled on several other unix's with small changes to the Makefile. Cheers, Craig "If God had meant us to be naked, we would have been born that way." Craig Taverner Structural Chemistry, University of the Witwatersrand, South Africa ------------------------------------------------------------------------------ 5) program VOLUME from raman@bioc01.uthscsa.edu In my opinion, the best program to do volume calculations on Protein structures is that written by Fred Richards (Yale U.) called VOLUME. It employs the Voronoi method to accomplish the volume calculations. You can obtain the source from Patrick Fleming: fleming@cs.yale.edu. It can be compiled with ease on any Unix platform. Cheers -raman C.S.RAMAN Department of Biochemistry University of Texas Health Science Center 7703 Floyd Curl Drive San Antonio, TX 78284-7760 USA Tel: (210) 567-6623 Fax: (210) 567-6595 E-mail: raman@bioc01.uthscsa.edu From uli@smaug.physics.mun.ca Fri Nov 24 12:07:26 1995 Received: from smaug.physics.mun.ca for uli@smaug.physics.mun.ca by www.ccl.net (8.6.10/950822.1) id MAA21458; Fri, 24 Nov 1995 12:01:27 -0500 Received: by smaug.physics.mun.ca (940816.SGI.8.6.9/911001.SGI) id NAA24144; Fri, 24 Nov 1995 13:31:00 -0330 Date: Fri, 24 Nov 1995 13:22:28 -0330 (NST) From: Uli Salzner Subject: DFT/spurious integrated densities To: ccl Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, I am trying to run routine DFT (LSDA) calculations with G92.The jobs frequently bomb because of spurious integrated densities. I got around the problem a couple of times by lowering the SCF convergence criterion or altering the geometry a little bit. This is not very satisfactory and it doesn't always work. Is there a "right" way to handle this? Would the same thing happen with G94? I would appreciate any comments. Thanks in advance Uli Salzner uli@smaug.physics.mun.ca From rafapa@obelix.cica.es Fri Nov 24 12:37:27 1995 Received: from obelix.cica.es for rafapa@obelix.cica.es by www.ccl.net (8.6.10/950822.1) id MAA21850; Fri, 24 Nov 1995 12:35:13 -0500 Received: (from rafapa@localhost) by obelix.cica.es (8.7.1/8.7.1) id SAA00598 for chemistry@www.ccl.net; Fri, 24 Nov 1995 18:31:32 +0100 (GMT-1:00) From: Rafael Rodriguez Pappalardo Message-Id: <199511241731.SAA00598@obelix.cica.es> Subject: statistical error in simulations To: chemistry@www.ccl.net Date: Fri, 24 Nov 1995 18:31:29 +0100 (MET) X-Mailer: ELM [version 2.4 PL24] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hello everybody! just a question, I'm looking for references about calculation of errors in quantities like RDF, running integration numbers,... obtained by means of MD/MC simulations. Can anyone help me? Best regards, Rafael