From GOVENDEM@che.und.ac.za Sun Jul 28 15:07:16 1993 Message-Id: To: CHEMISTRY@ccl.net From: GOVENDEM@che.und.ac.za Date: 28 Jul 93 13:07:16 +0200 (SAST) Subject: Help with G92 frequency calculation Dear netters, I am working on the interaction between methanol and dimethylether. Using the Gaussian92 program I have optimized the structure at the MP2 level,using the 6-31G** basis set.However I have had no luck in attempting a frequency calculation on this optimized structure. The termination signal I get is:FORTRAN I/O :COULD NOT OPEN FILE SPECIFIED.I have tried to overcome this problem using the following control cards: #N MP2(MAXDISK=80000000)/6-31G** FREQ SCF=DIRECT OPTCYC=100 but to no avail. Does anyone have any suggestions? Thanks Bradley From nmills@alchemy.chem.trinity.edu Tue Jul 27 22:31:25 1993 Date: Wed, 28 Jul 93 03:31:25 -0500 From: nmills@alchemy.chem.trinity.edu (nancy mills) Message-Id: <9307280831.AA08082@alchemy.chem.trinity.edu> To: CHEMISTRY@ccl.net Subject: Use of MM3(92) on SGI I understand from Richard Counts that the version of MM3(92) for the IBM RS6000 which is available from QCPE should be easily portable to the SGI (we have a Personal Iris 4D30G). Is anyone running MM3 on an SGI and can a person with minimal UNIX expertise port it over? Thanks for your help. Nancy Mills, Trinity University nmills@trinity.edu From DWARKNTH@ACFcluster.NYU.EDU Wed Jul 28 04:09:10 1993 Date: Wed, 28 Jul 1993 09:09:10 -0500 (EST) From: DWARKNTH@ACFcluster.NYU.EDU Subject: RE:Unwinding DNA ? To: chemistry@ccl.net Message-Id: <01H12JMLNA2QV7QYWP@ACFcluster.NYU.EDU> Sorry for my error in typing Tom Wiese's name.I apologise for the same. Sulatha. ___________________________________________________________________________ Sulatha Dwarakanath Dept. Of Biology New York University NY 10003. E-Mail:dwarknth@acfcluster.nyu.edu ___________________________________________________________________________ From adit@Kodak.COM Wed Jul 28 04:37:36 1993 Date: Wed, 28 Jul 93 08:37:36 EDT From: adit@Kodak.COM (Adi Treasurywala) Message-Id: <9307281237.AA07346@bcc9.kodak.com> To: chemistry@ccl.net Subject: Scanned Structures: SUMMARY. Folks, Thanks for all the e-mail. I got MANY responses. Thank you to all who responded. The summary however need be very short. It seems that the clear winner was a program called KEKULE. The details are enclosed. The close second was described best in the enclosed mail from the author Peter Johnson. Then there were miscellaneous one-shot mentions that I will skip for now. If anyone is interested in a complete transcript please let me know within a week or so. ORIGINAL QUESTION: > Folks, > Maybe I was just dreaming but it seems to me some time ago that > someone either had or was looking for a piece of software that > would allow one to scan in 2D structures (from say a > publication) and make mol files from the info. If anyone has > any information on such a program I would appreciate hearing > from them. The platform is not too important. In the RARE event > that there is a substantial response I will summarize for the > net of course. > > Thanks in advance for your help. > > Adi M Treasurywala,Sterling Winthrop Inc,1250 South Collegeville Road, > PO Box 5000, Collegeville, PA 19426-0900,Voice (215)983-6610 FAX > (215)983-5559, INTERNET adit@kodak.com KEKULE: J. Chem. Inf. Comput. Sci., 32(4), 373-8, "Kekule: OCR-optical chemical (structure) recoginition > You were not dreaming: > > Kekule converts scanned images into almost any format for chemical structures. > It runs on a PC under Windows 3.1 > > List price:$2900 but "on sale" now for $895 > > Contact: > > PSI International Inc. > 810 Gleneagles Court, Suite 300 > Towson, MD 21286 > (410) 821-5980 > > This software was reviewed in Chemical and Engineering News pp 17-19, > March 23, 1992. > > --keith > > Dr. Keith MaloneyHuss > SmithKline Beecham Pharmaceuticals > CLiDE: > There are two systems which do exactly the job you have specified. > These are KEKULE marketed by a company called PSI International > which operated from Baltimore MD. This software runs on macintosh > and PC compatibles. The other has been developed here at the > University of Leeds and is called CLiDE. This software currently > runs on a SUN workstation, but there are plans to port to other > platforms. A description of our system as it stood a year ago is > found in j,Chem.Inf.Comput.Sci. 1993,33, 338-344. > Peter Johnson > School of Chemistry > University of Leeds > Thanks again, Adi. From gene@calv2.cray.com Wed Jul 28 06:01:02 1993 Date: Wed, 28 Jul 93 10:01:02 EDT From: gene@eastrg2.cray.com (Eugene Fleischmann) Message-Id: <9307281401.AA25000@eastrg2.cray.com> To: chemistry@ccl.net Subject: Re: Transition state opt. in CADPAC Pertinent keywords: OPTIMISE SADDLE BERNY Sample job deck follows: Gene ++++++++++++++++++++++++++++++++++++++++ Eugene D. Fleischmann, Ph.D. Computational Chemist Cray Research, Inc. (301)595-2695 gene@eastrg2.cray.com ++++++++++++++++++++++++++++++++++++++++ MAXMEM 3000000 CALC TITLE Chloroform CHARGE 0 MULTIPLICITY 1 DIHEDRAL NEW VARIABLES BOND2 1.020000 A BOND3 1.760000 A BOND4 1.760000 A BOND5 1.760000 A ANGLE3 109.500000 D ANGLE4 109.500000 D ANGLE5 109.500000 D TOR3 0.000000 D TOR4 -120.000000 D TOR5 120.000000 D END ATOMS X -1 1 0 0 Y -1 0 1 0 Z -1 0.000000 0.000000 -1.020000 C1 6 0 0 0 LIBRARY CSTO3G END H2 1 LC C1 Z BOND2 LIBRARY HSTO3G END Cl3 17 TCT C1 H2 X BOND3 ANGLE3 TOR3 LIBRARY CLSTO3G END Cl4 17 TCT C1 H2 Cl3 BOND4 ANGLE4 TOR4 LIBRARY CLSTO3G END Cl5 17 TCT C1 H2 Cl3 BOND5 ANGLE5 TOR5 LIBRARY CLSTO3G END END CLOSED CONVERGE 7 MAXIT 50 GUESS MINGUESS DIIS ON SECDER START FCM OPTIMIZE SADDLE BFGS SKIP INTEGRALS SCF NUMGRAD 10 GRADTOL 4 START ORIGIN COM PROPERTY START FINISH From mwd@carina.cray.com Wed Jul 28 05:51:25 1993 From: mwd@carina.cray.com (Mark Dalton) Message-Id: <9307281551.AA27359@calamity> Subject: Summary for: 3D substructure searching To: CHEMISTRY@ccl.net Date: Wed, 28 Jul 93 10:51:25 CDT This is a bit long and I tried to summerize as simply as posible. I am summerizing by request and am try to show concensus, (Basicly, my company is not responsible for these actions). Thanks! Mark Original post: >From: mwd@carina.cray.com (Mark Dalton) >Subject:3D substructure searching >Date: Fri, 23 Jul 1993 12:31:51 -0500 (CDT) >Message-ID:<9307231731.AA11648@calamity> >Hi! > > Does anyone know of a program that will take a known 3D structure >or substructure and be able to search the PDB for similar 3D structures or >substructures? Or even search a substructure against a single structure? > >I don't think the MULTI package does what I need, I think that will >take a predict the structure of a unknown structure by comparing the primary >sequence with a known structure, or a profile of substructures. > >Any information would be appreciated. > >Thanks! > >Mark The answers were: 1. PROTEP - PROtein Topographic Exploration Programs PROTEP is a powerful method for finding relationships among protein structures. It performs similarity searches on the entire Brookhaven Protein Data Bank in a matter of minutes (on an SGI 4d/35). It was developed at Sheffield University by Professor Peter Willett, Dr. Pete Artymiuk and Dr. David Rice. PROTEP brings the formidable power of the branch of mathematics called Graph Theory to bear on the problem of ultra rapid 3D structural comparison. The PROTEP command gives you access to the various functions of the PROTEP software that can be run from within SYBYL. It also allows you to display the results of a PROTEP Motif Search at the SYBYL display. Tripos Associates 800-323-2960 This allows substructure searches based on protein secondary structure elements. You input a pattern of secondary structures in 3-D space and a complete search of the PDB takes about 5-10 mins for a substructure search or 20 mins for a maximal common subgraph search - where a user-specifed number of secondary structure elements must be in common - searches can be performed with whole proteins or just elements extracted from proteins (or made up patterns) - search is independent of sequence although you can specify that the hits must be in the same sequence order - for strands in a sheet for example. We are also testing a residue-based version of the above that allows similar searches but this time for patterns of residues in 3-D space so you can search for active sites etc. - this is working fine, but not yet marketed - search times are similar to above - on SGI 3000 type machine. 2. Oxford Molecular market IDITIS - developed at Birkbeck College, London under Janet Thornton - this is a relational database-type product that is totally different to our approach but may do what you want. 3. WHATIF, by Vriend at EMBL, Heidelberg. 4. CAVEAT - assist in the structure-based drug design process, to help chemists identify templates and molecule fragments that could be used to hold functional groups or chains in a particular orientation, but there are many other applications for it. In particular, I would be very excited to see someone apply it to searches in the PDB; it is ideally suited for certain types of searches, but we simply haven't identified a specific problem yet to apply it to. (See below for more detail). 5. CAVEAT, as well as the companion program CLASS (that further screens and clusters CAVEAT hits) and TRIAD and ILIAD (which are 3D databases representing comprehensive collections of computed, minimized structures) are available through license from the University. 6. MDL has two programs which do 3D substructure searching over user-created 3D databases - MACCS-3D and ISIS-3D (which is distributed). These allow searching for 2D and 3D substructure fragments, which can also be constrained by distances, angles, dihedrals, planes, lines, normals, and exclusion spheres. They allow static and conformationally flexible searching (via torsional optimization and relaxation). (Steve Muskal, formerly with Sung Ho Kim at UCB), who developed an application where he stored alpha carbon backbones only, and searched for motifs using our regular 3D substructure searching capability. He can be reached at SteveM@molecular.com. 3D SSS are mainly designed for drug-molecule searching, like ours is These programs include: Aladdin (Daylight Chemical Information systems) Sybyl-3DB Unity (Tripos) ChemDBS-3D (Chemical Design) Cambridge Crystallographic DB and software Caveat (Paul Bartlett, UC Berkeley) Catalyst (Biocad) DOCK (Tak Kuntz, UCSF) 7. DEJAVU - Secondary Structure Motif Analysis DEJAVU will take a description of the secondary structure elements that occur in your particular protein and compare it to a huge database of secondary structure elements that occur in protein structures that have been published as PDB files. Other info: References: F. C. Bernstein, T. F. Koetzle, G. J. B., Williams, E. F. Meyer, Jr., M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, & M. Tasumi, "The Protein Data Bank: A Computer-based Archival File for Macromolecular Structures:, J. Mol. Biol. 112, 535-542 (1977). S. F. Altschul, W. Gish, W. Miller, E. W. Myers, & D. J. Lipman, "Basic Local Alignment Search Tool", J. Mol. Biol. 215, 403-410 (1990). Martin, Bures, and Willett, "Searching Databases of 3D Structures", in Boyd and Lipkowitz, ed, Reviews in Computational Chemistry, Vol 1, VCH, 1990, 213-264. A few academics have worked in the area - most notable is Peter Willett - a literature search on his name will yield a few references describing his protein searching software. 1. Date: Mon, 26 Jul 1993 10:21:07 +0100 From: Johan Postma Subject: 3D substructure searching Hi, we are working on a "PDB access system" for several years. The project is now in a final stage. We do have a 3D-"motif" search program (i.e. search for typical strands/helices) but this could be extended (easily). As an example we took the Colicin A helices (it;s know that 6 helices form a "globin" fold and browsed through the complete PDB-database (more then 1000 entries) and were able to find all the globins in approximately 10 CPU seconds (VAX9000) We certainly would be interested to try out other 3D-structure searches in order to test and tune our PDB-access mechanism. Let me know if you are interested. Johan Postma EMBL (European Molecular Biology Laboratory) Heidelberg Germany 2. Date: Sun, 25 Jul 93 18:20:48 CDT From: states@ibc.wustl.edu (David J. States) There are two distinct problems in substructure matching. The first is search for similar 3-D substructures assuming that you know the linear order of bonding. There are a variety of programs that do this dating back to the 70s and some early work by Argos, Maclachlan (sp?), Sanders, and others. Basic approach is to create a sequence of internal coordinate values and to use standard sequence similarity search algorithms. I don't follow the packages much, but some of the molecular modeling programs probably have this capability built in. A related approach is to classify substructures and then look for similar sequences of class assignments along the backbone. Larry Hunter and I have done some work on this, but you should also look at Rooman&Wodak, Liebman (various papers) and Unger&Sussman. The second problem is looking for similar packing patterns in arbitrarily ordered sets of atoms. The most insteresting apporach to this that I have seen is from Fischer, Bachar, Nussivno, and Wolfson (Journal of Biomolecular Structure and Dynamics (1992) 9:769-89). They build a distance tuple table and use it for efficient look up of similar sbustructures that are independent of bonding or atom order. Borrows heavily on machine vision work. I would be interested in other responses you get. David States Insitute for Biomedical Computing / Washington University in St. Louis 3. Date: Sat, 24 Jul 1993 15:20:03 +0300 (MET-DST) From: GERARD@XRAY.BMC.UU.SE (Gerard Kleijwegt a.k.a. gerard@xray.bmc.uu.se) Dear Mark, your question wasn't quite clear:- do you want to look for a substructure in the sense of a collection of atoms, or for a motif, i.e. a set of helices and strands ? In the latter case, I have written a program called DEJAVU which will do just that. If you're interested, I can send you the manual. --Gerard Kleywegt Dept Molecular Biology Univ of Uppsala Uppsala, SWEDEN From: yee@gold.cchem.berkeley.edu (Raymond Yee) Date: Fri, 23 Jul 1993 22:27:07 +22306404 (PDT) Hi Mark, You may be interested in the following extract from a file that one can get from the Brookhaven protein databank (I think that's where I got it anyhow). I'm sending you the top part of the file (with the references and a sample of what it is.) You can try to find more info about it. If you'd like, I could send you the entire file that I have (it's about 50K long.) Good luck, Raymond The file is called seq_groups.jan.93 Here's the extract: /* This file was compiled by Laura Lynn Walsh, Beckman Institute, University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801-2325 (217) 244-6764 lwalsh@nemo.life.uiuc.edu Suggested citation for use of this file is: L. L. Walsh, "Sequence Groups Derived from BLAST", personal communication, (1993). Date begun: Jan, 1993 Latest revision: May, 1993 (includes Jan, 1993 update) */ /* References: F. C. Bernstein, T. F. Koetzle, G. J. B., Williams, E. F. Meyer, Jr., M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, & M. Tasumi, "The Protein Data Bank: A Computer-based Archival File for Macromolecular Structures:, J. Mol. Biol. 112, 535-542 (1977). S. F. Altschul, W. Gish, W. Miller, E. W. Myers, & D. J. Lipman, "Basic Local Alignment Search Tool", J. Mol. Biol. 215, 403-410 (1990). */ /* This file was obtained by first running BLAST on the entire release of the Protein Data Bank, including the pre-release files. The sequences were taken from the SEQRES records of each file, a BLAST database was made of them, and then each sequence was in turn run against the whole database. From those sequences which were identical (same length, same gaps, if any), only one sequence was retained. A second "unique" data base was made and each sequence was again run against the whole data base. The sequence groups were obtained by grouping together all sequences with identities greater than 50%. These sequence groups were associated together if there was lesser, but still significant homology between them. Associated groups are separated by dotted lines. Unrelated groups are separated with solid lines. In a few sequence groups, e.g. the immunoglobulins, the homologies are not completely transitive. Protein A may be 50% identical to protein B and protein B may be 50% identical to protein C, but protein A is not 50% identical to protein C. In that case, a given protein was added to the group if it was 50% identical to at least one protein that was already in the group. NOTE: Peptides shorter than 20 amino acids frequently have homologies to segments of several otherwise unrelated proteins. These are thought to be statistically insignificant. */ [rest of file deleted] From DOUGH@molecular.com Mon Jul 26 12:49:03 1993 Subject: 3D substructure searching Although some people have done work in searching for motifs in 3D protein databases, the problem of finding a given substructure still falls in the domain of smaller-molecule 3D substructure searching. A review of that field can be found in Martin, Bures, and Willett, "Searching Databases of 3D Structures", in Boyd and Lipkowitz, ed, Reviews in Computational Chemistry, Vol 1, VCH, 1990, 213-264. MDL, for whom I work, has two programs which do 3D substructure searching over user-created 3D databases - MACCS-3D and ISIS-3D (which is distributed). These allow searching for 2D and 3D substructure fragments, which can also be constrained by distances, angles, dihedrals, planes, lines, normals, and exclusion spheres. They allow static and conformationally flexible searching (via torsional optimization and relaxation). All that is the good news.... the bad news is that they are limited to 256 heavy atoms - fine for drug companies, but not for PDB-sized files. We actually have someone here (Steve Muskal, formerly with Sung Ho Kim at UCB), who developed an application where he stored alpha carbon backbones only, and searched for motifs using our regular 3D substructure searching capability. He can be reached at SteveM@molecular.com I believe your company has already opened some kind of relationship with MDL, though I doubt you have any of our programs in-house. At present, the main other programs I know of which do 3D SSS are mainly designed for drug-molecule searching, like ours is. These programs include: Aladdin (Daylight Chemical Information systems) Sybyl-3DB Unity (Tripos) ChemDBS-3D (Chemical Design) Cambridge Crystallographic DB and software Caveat (Paul Bartlett, UC Berkeley) Catalyst (Biocad) DOCK (Tak Kuntz, UCSF) A few academics have worked in the area - most notable is Peter Willett - a literature search on his name will yield a few references describing his protein searching software. I can be reached at: Doug Henry MDL 2132 Farallon Drive San Leandro, CA 94577 (510) 895-1313 xt 1316 dough@molecular.com Date: Mon, 26 Jul 1993 17:29:15 +0300 (MET-DST) From: GERARD@XRAY.BMC.UU.SE (Gerard Kleijwegt a.k.a. gerard@xray.bmc.uu.se) Subject: Re: PDB searching I'm sending you the manual as the next mail. In order to run DEJAVU you would need to have 'O' (successor to FRODO), although it's not strictly necessary. If you have a particular protein, i could run the program for you if you send me a PDB file. If you want to obain the software, please contact Prof Alwyn Jones (e-mail: "alwyn@xray.bmc.uu.se") first (he does the licensing stuff). If you want to inform others, no problemo. Note that the software is free for academic users with a valid O-license; an O-license can be obtained from prof Jones. For non-academic users there is a charge. Stand by for the manual ... --Gerard (I did not forward the manual to list do to the length) if you are interested I will forward it to individuals - mwd@carina.cray.com). Gerard Kleywegt Dept. of Molecular Biology Biomedical Centre University of Uppsala DEJAVU will take a description of the secondary structure elements that occur in your particular protein and compare it to a huge database of secondary structure elements that occur in protein structures that have been published as PDB files. What's the basic idea ? A MOTIF of secondary structure elements (henceforth abbreviated "SSEs") consists of N SSEs, each of which comprises M(i) residues and has a length of L(i) Angstrom (measured from the first residue's Calpha to that of the last residue), and which is characterised by a matrix D(i,j) which contains the centre-to-centre distances (for example) and by another matrix C(i,j) which contains the cosines of the angles made by the direction vectors of the individual elements (the direction vector goes FROM the N-terminal Calpha TO the C-terminal one). Finding a motif in the database that is SIMILAR to that which occurs in your protein then comes down to finding suitable collections of N SSEs in the structures of other proteins which have approximately the same numbers of residues, the same lengths and comparable mutual distances and direction-vector cosines. And that is ALL there is to it ! (1) CONTENTS ============ 1 - contents 2 - introduction 3 - user input files 4 - running the program 5 - finding a motif 6 - analysing the results 7 - a realistic example 8 - automatic creation of input files 9 - detailed analysis of results on cro 10 - miscellaneous 11 - release notes 12 - select option 13 - incremental search example 14 - topology option 15 - installing the software 16 - running the software Date: Mon, 26 Jul 1993 15:30:06 -0500 (CDT) From: David Larson I am using Sybyl 6.0, Tripos Associates, on Silicon Graphics workstations, and their latest release includes an interface to the program PROTEP. Here is their blurb on PROTEP from the Help utility: PROTEP PROtein Topographic Exploration Programs PROTEP is a powerful method for finding relationships among protein structures. It performs similarity searches on the entire Brookhaven Protein Data Bank in a matter of minutes (on an SGI 4d/35). It was developed at Sheffield University by Professor Peter Willett, Dr. Pete Artymiuk and Dr. David Rice. PROTEP brings the formidable power of the branch of mathematics called Graph Theory to bear on the problem of ultra rapid 3D structural comparison. The PROTEP command gives you access to the various functions of the PROTEP software that can be run from within SYBYL. It also allows you to display the results of a PROTEP Motif Search at the SYBYL display. Tripos Associates 800-323-2960 Hope this helps. Best regards, Dave Larson ------------------------------------------------------------------------------- Dave Larson | Image Analysis Facility, 70 EMRB University of Iowa | Iowa City, IA 52242 larson@caesar.iaf.uiowa.edu | (319) 335-7900 ------------------------------------------------------------------------------- Thanks to: tucker@ERE.UMontreal.CA (Carrington Tucker) I found out about Paul A. Bartlett: Date: Mon, 26 Jul 93 16:25:37 -0700 From: paul@fire.cchem.berkeley.edu (Paul A. Bartlett) Dear Mark, Yes, you have the right Bartlett. We have developed a program for identifying 3D similarities between molecules, and that can be used on structures within the PDB. We originally developed the program CAVEAT to assist in the structure-based drug design process, to help chemists identify templates and molecule fragments that could be used to hold functional groups or chains in a particular orientation, but there are many other applications for it. In particular, I would be very excited to see someone apply it to searches in the PDB; it is ideally suited for certain types of searches, but we simply haven't identified a specific problem yet to apply it to. CAVEAT was developed specifically for searching for structural similarities that can be defined as a relationship between bonds and their orientations, in contrast to the more traditional search algorithms that are based on relationships between atoms and their distances. Basically, for a given set of bonds in a molecule (user- selected), which we treat as vectors, we calculate the relationship between all the pairs and incorporate this information in what we call a "vector database". This database is in reality an index to the source database, with the molecules characterized by bond relationships instead of atomic coordinates and connectivities. It is then a relatively quick process to search for molecules that have in common a particular relationship among bonds. For specific application to protein structures, we have made a variety of vector databases. For example, in one instance, we have taken all the pair-wise combinations of C-alpha to C-beta bonds, within a specified radius (e.g., 20 Angstroms). We can define almost any type of secondary structure through a combination of such vectors, and then look through the PDB for other proteins that may have the same structural element, independent of the identity of the amino acid side chains themselves or their connectivity (the relationship need not involve contiguous residues). Or we can define a vector-database with the C- beta to C-gamma bonds, and look for similiarities between side-chain conformers. A database constructed from carbonyl C=O bonds might be useful for probing backbone similarities, etc. There also exists the opportunity for flexible definition of tolerances; for example, in a single search, one can look for an alpha-helix (perhaps 3-5 side-chains, tightly defined) and a beta-sheet (similarly, a few side-chains with limited tolerance) and a particular relationship between them (pairing vectors in one with vectors from another with looser tolerances). The searches are relatively quick, typically less than a minute or two on an SGI R3000 Indigo (sorry, a Cray is not necessary), and the program can handle any number and combination of vectors. In spite of its origin, there are many ways to use CAVEAT; indeed, I'm sure there are a lot that we haven't thought of yet! Fundamentally, any search that you can define as a 3-dimensional relationship between bonds can probably be cast as a CAVEAT search. CAVEAT, as well as the companion program CLASS (that further screens and clusters CAVEAT hits) and TRIAD and ILIAD (which are 3D databases representing comprehensive collections of computed, minimized structures) are available through license from the University. I have probably gone on longer than you need (or anticipated...), but I am happy to provide additional information if you wish. You know my e- mail address, and you can reach me by phone (510-642-1259) or FAX (642- 1454). Cheers, Paul From: A Poirrette Date: Tue, 27 Jul 93 15:34:26 BST Mark, TRIPOS ASSOCIATES INC. market a program called PROTEP that we developed here in Sheffield. This allows substructure searches based on protein secondary structure elements. You input a pattern of secondary structures in 3-D space and a complete search of the PDB takes about 5-10 mins for a substructure search or 20 mins for a maximal common subgraph search - where a user-specifed number of secondary structure elements must be in common - searches can be performed with whole proteins or just elements extracted from proteins (or made up patterns) - search is independent of sequence although you can specify that the hits must be in the same sequence order - for strands in a sheet for example. We are also testing a residue-based version of the above that allows similar searches but this time for patterns of residues in 3-D space so you can search for active sites etc. - this is working fine, but not yet marketed - search times are similar to above - on SGI 3000 type machine. Also Oxford Molecular market IDITIS - developed at Birkbeck College, London under Janet Thornton - this is a relational database-type product that is totally different to our approach but may do what you want. Also a program, WHATIF, by Vriend at EMBL, Heidelberg, may do what you want. Hope this helps Andrew Poirrette Department of Information Studies University of Sheffield UK -- Mark Dalton AUG-GCU-AGA-AAG H Cray Research, Inc. M A R K | Eagan, MN 55121 CH3-S-CH2-CH2-C-COOH Internet: mwd@cray.com | (612)683-3035 NH2 From JKONG@ac.dal.ca Wed Jul 28 11:01:51 1993 Date: Wed, 28 Jul 1993 14:01:51 -0300 From: JKONG@ac.dal.ca Subject: ? limit of file systems on IBM RISC/6000 To: chemistry@ccl.net Message-Id: <01H12TXELQJM009TRW@AC.DAL.CA> Dear netters, We sent an enquiry a week ago about queueing system of IBM/RS6000 to this lovely net and got many helpful replies and I will summarize them and probably bug some fellows later on. This is posting another question about the size limitation of file systems in the same operating system. I remember that someone asked about how to break the file-size limit of 2G bytes. My question is how to mount more than 2G bytes disk space for one file system, say /tmp. We couldn't increase the size of /tmp to more than 2G bytes. We called IBM people and were told that it's the limit of file systems for a 32-bit computer. But if the file entry in an i-node is 32 bits, the possible file-size should be 4G blocks or 2G blocks if one bit is used for other purpose. The only problem I can speculate so far is that the operating system could be confused when it tries to report in byte the file-size of a file bigger than 4G or 2G bytes. Do any people know how to overcome this prolem? Or do we have to spread temporary files in several file systems? We are running Gaussian 92 and a CI package and need lots of temporary disk space. Thank you in advance. Jing Kong From d3f012@pellucidar.pnl.gov Wed Jul 28 07:41:45 1993 Date: Wed, 28 Jul 93 14:41:45 -0700 From: d3f012@pellucidar.pnl.gov Subject: MNDO/AM1/PM3 parameters? To: chemistry@ccl.net Message-Id: <9307282141.AA14071@pellucidar.pnl.gov> Have MNDO/AM1/PM3 paramters ever been developed for Na, Mb, K, Ca, Rb, Sr, Cs,...etc? Mark Thompson ************************************************************************** Mark A. Thompson Sr. Research Scientist email: d3f012@pnlg.pnl.gov Molecular Science Research Center FAX : 509-375-6631 Pacific Northwest Laboratory voice: 509-375-6734 PO Box 999, Mail Stop K1-90 Richland, WA. 99352 Argus available via anonymous ftp from pnlg.pnl.gov (130.20.64.11) (in the argus directory). Download the README file first. Disclaimer: The views expressed in this message are solely my own and do not represent Battelle Memorial Institute, Pacific Northwest Laboratory, or any of its clients. ************************************************************************** From ALLEY@vaxc.cc.monash.edu.au Mon Jul 29 20:02:47 1993 Date: 29 Jul 1993 10:02:47 +1000 From: ALLEY@vaxc.cc.monash.edu.au Subject: molecular modelling query summary responses To: chemistry@ccl.net Message-Id: <01H13ZYFVT6A8WX7BY@vaxc.cc.monash.edu.au> Dear Netters, Thankyou to all those who replied to my query about molecular modelling. I have included below a list of the software packages which were mentioned. The packages were: 1. Amber 2. Charmm 3. Discover 4. Grid 5. Biosym. Thankyou again for your assistance, Lisa Alley.