From DEPAZ@vm1.sdi.uam.es Wed Nov 8 03:47:13 1995 Received: from vm1.sdi.uam.es for DEPAZ@vm1.sdi.uam.es by www.ccl.net (8.6.10/950822.1) id DAA28757; Wed, 8 Nov 1995 03:42:38 -0500 Message-Id: <199511080842.DAA28757@www.ccl.net> Received: from vm1.sdi.uam.es by vm1.sdi.uam.es (IBM VM SMTP V2R2) with BSMTP id 2787; Wed, 08 Nov 95 09:41:03 HOE Received: from vm1.sdi.uam.es (DEPAZ) by vm1.sdi.uam.es (Mailer R2.08) with BSMTP id 6217; Wed, 08 Nov 95 09:41:02 HOE Date: Wed, 08 Nov 95 09:34:01 HOE From: "Dr. Jose Luis Garcia de Paz" Organization: Native address: Subject: conversion between different document formats To: Computational chemistry list Dear CCL'er, I have been working with an IBM VM/CMS system. I have many chemistry documents wirtten using IBM SCRIPT/VS. Now, our IBM VM/CMS computer will be substituted by an UNIX computer. Also the former uses ebcdic and the unix uses ascii. Please, do you know where can i get a freeware (or very cheap) program that may convert an IBM script file in (i.e.): a) html file; b) LaTEX file; c) Wordperfect file . Really, I need do not loose my script files. Any conversor will be welcome. For me, is the same a pc program or an unix program. Thank you. Regards, Jose Dr. Jose Luis Garcia de Paz (34) (1) 3974957. FAX (34) (1) 3974512. (34) (1) 3974263. Departamento de Quimica Fisica Aplicada. FACULTAD DE CIENCIAS, C-XIV-602. Universidad Autonoma de MAdrid. 28049-Madrid (Spain). From wes@orgf5.bmc.uu.se Wed Nov 8 04:33:14 1995 Received: from columba.udac.uu.se for wes@orgf5.bmc.uu.se by www.ccl.net (8.6.10/950822.1) id EAA29034; Wed, 8 Nov 1995 04:26:30 -0500 Received: from ORGF5.bmc.uu.se by columba.udac.uu.se with SMTP id AA22008 (5.67b/IDA-1.4.4 for chemistry@www.ccl.net); Wed, 8 Nov 1995 10:26:00 +0100 Received: by orgf5.bmc.uu.se (950911.SGI.8.6.12.PATCH825/940406.SGI) id KAA10776; Wed, 8 Nov 1995 10:21:14 +0100 Date: Wed, 8 Nov 1995 10:21:14 +0100 From: wes@orgf5.bmc.uu.se (Wesley Schaal) Message-Id: <199511080921.KAA10776@orgf5.bmc.uu.se> To: "Dr. Jose Luis Garcia de Paz" Cc: Computational chemistry list Subject: Re: CCL:conversion between different document formats In-Reply-To: <4617484@toto.iv> Jose Luis Garcia de Paz writes: > Dear CCL'er, > I have been working with an IBM VM/CMS system. I have many chemistry > documents wirtten using IBM SCRIPT/VS. Now, our IBM VM/CMS computer > will be substituted by an UNIX computer. Also the former uses ebcdic > and the unix uses ascii. > Please, do you know where can i get a freeware (or very cheap) program > that may convert an IBM script file in (i.e.): a) html file; b) LaTEX file; > c) Wordperfect file . Really, I need do not loose my script files. > Any conversor will be welcome. > > For me, is the same a pc program or an unix program. Thank you. Regards, > Jose > The standard unix utility "dd" will convert the plain text (html, LaTEX) for you. Look at the man page for details but you'll need to do something like this: dd if=inputfile of=outputfile conv=ascii to convert from ebcdic to ascii. -- Wesley Schaal, wes@orgf5.bmc.uu.se Organic Pharmaceutical Chemistry BMC, Uppsala University, Sweden From martin.norin@sto.pharmacia.se Wed Nov 8 08:02:15 1995 Received: from gatekeeper.pharmacia.se for martin.norin@sto.pharmacia.se by www.ccl.net (8.6.10/950822.1) id HAA01385; Wed, 8 Nov 1995 07:58:42 -0500 Received: from mailgate.pharmacia.se by gatekeeper.pharmacia.se; (5.65/1.1.8.2/16Feb95/sal) id AA28569; Wed, 8 Nov 1995 14:03:06 +0100 Received: by mailgate.pharmacia.se (5.65/DEC-Ultrix/4.3/sal-950131) id AA26147; Wed, 8 Nov 1995 13:53:08 +0100 Date: Wed, 8 Nov 1995 13:53:08 +0100 Received: from umc by mailgate.pharmacia.se via MR/PHAROS with conversational-MRIF; Wed, 08 Nov 95 13:53:07 +0100 Posted: Wed, 08 Nov 95 13:49:37 +0100 Sender: martin.norin@sto.pharmacia.se From: "NOYM" Message-Id: <9936491308111995/A03103/MEANIE> App-Message-Id: <9936491308111995/A03103/MEANIE/119B436E2200> To: "Michael Sundstrom" , "Bjorn Nilsson" , "Tomas Lundqvist" , "Per Kraulis" , "Johan Kordel" , "Mats Kihlen" , "Mats Dahlberg" , "Comp.Chem.List" Subject: Summary-Compressed PDB Lists. Sensitivity: Company-Confidential Dear Colleagues, Thank you all for the replies to my question about a compressed pdb-list. They have been very useful for me. ===================================================================== The PDB directory currently consists of about 3800 records. However, many of these are different versions of the same structures (for example different mutants of the same protein or one protein with a number of different ligands or a lot of DNA/RNA structures). It would, for a number of reasons, be very valuable to have a subset of the PDB containing representatives ("the best structure") of each unique protein, and important conformers. If anybody have done a comprehensive investigation to compile such a list or if it is already available on the net please let me now ! I'm also interrested in any hints how to do this without manually going through every record in the PDB. ====================================================================== Here follows a summary: ====================================================================== CATH: You can also get similar information from our CATH web page, where Chris Orengo and Alex Michie have developed a hierarchical numbering system for related folds and sequences. I suggest starting with http://www.biochem.ucl.ac.uk/bsm/biocomp/index.html rob. ----|------ My comment: Take a look at this site if your into bioinformatics ! it contains structural classifications of proteins ( like in SCOP), algorithms for threading etc. ----|------ My comment again: Take also a look at the SCOP database (http:// scop.mrc-lmb.cam.ac.uk/scop/) ! ====================================================================== PDB_SELECT lists from the EMBL: Hi, It's been done by many people. Perhaps best by Sander's group at EMBL. You can get their latest PDB_SELECT lists from the EMBL file server (ftp.embl-heidelberg.de). A reference describing their method is Protein Science, 1, 409 ' 92. Hope this helps (or keeps you from redoing it yourself!), Jay Ponder, Washington Univ, St. Louis ====================================================================== DALI: Comparison of protein structures in 3D: I believe Chris Sander at EMBL has already done similar work (Hobohm & Sander, Protein Sci., 1994, 3:522-544) which should be accessible via the Net/Web at http://www.sander.embl-heidelberg.de. Good luck, Scott ----|------ My comment: This site should also be checked if your into bioinformatics: Below is a text I've extracted from the DALI web site (http://www.sander.embl-heidelberg.de). Here you also find a map of proein structure relations in a clustering diagram (look at the FSSP database): "The Dali server The Dali server is a network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank. A multiple alignment of structural neighbours is mailed back to you. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. If you want to know the structural neighbours of a protein already in the Protein Data Bank, you can find them in the FSSP database. You can ... submit coordinates by email (recommended) submit coordinates interactively (experimental) read a paper about the Dali method read a review about structure searches send feedback to the Dali authors get help with the Dali server retrieve precalculated structural similarities from the FSSP database look at 3D views of examples of unexpected structural similarities look at statistics about WEB access to Dali " ----|------ General comment: Comment from Max Vasquez, Several such compilations have been published by Chris Sander's group at the EMBL-Heidelberg (check their web site for an updated list) as well as by others (I happen to have a reference by Orengo and co-workers in Protein Engineering 6, 485 [1993]). Just be aware that these compilations tend to be more compressed that one may bargain for. For example, just one or very few serine proteases are included, similarly for immunoglobulins, etc. Best wishes, Max Vasquez, PhD, ===================================================================== Laura Walsh Annotated PDB File Listing: Suggested citations for use of this file are: L. L. Walsh, "Annotated PDB File Listing", Protein Science 1:5, Diskette Appendix (1992). She has broken down the PDB by molecule or compound. The latest revision I have of the listing is April 1994. Does anyone know of a more up to date listing? Jeff Nauss ----|------ My comment: Yes, the most updated list may be found in Lauras reply below. This list is very useful even now in the web-era. It contains a list of each molecule in alphabetic order with the resolution and other important information of each record in the PDB. The only drawback is that I have not found any more recent updates than from the Jan 94 release (see below for info of this release): ----|------ I did this a year ago last August. The results can be obtained from my www site: http://www.scs.uiuc.edu/~lwalsh A citation for a paper published about the process is included in the Work in Progress Annotation. Laura Walsh, ----|------ Also available at: Did you have a look at files in CCL archives in: /pub/chemistry/documents/PDB/PDB_file_list on www.ccl.net ? Jan jkl@ccl.net ====================================================================== Commercial: ...It is also only part of the story, in that there are also inconsistent atom labeling, so that searches for a given structure won't always find all of those hits. I don't know what public domain fixes there are, but I do know that Oxford Molecular went through the PDB database, making it consistent and fixing up irregularities. They now offer it as relational database called Iditis, so you should try contacting them. Their web page is at: http://www.oxmol.co.uk/ or I you could send email to: roger@madison.polytechnique.fr Good luck, Ernest Chamot, ----|------ Comment from Pieter Stouten: I always wondered why they would use a relational database paradigm. Proteins are ordered and the information one wants to retrieve often involves stretches of residues with certain characteristics. Using a relational database, one needs to do many operations. It seems to me that a mixture of pattern matching (with additional bonus of easily allowing for a few mismatches) and relational operations would be much more efficient. Does anybody have any opinions about this? Thanks, Pieter Stouten . ===================================================================== ---------------------------------------------------------------------- Martin Norin, Ph.D. e-mail:martin.norin@sto.pharmacia.se Dept. Struct. Biochem. Pharmacia Biopharmaceuticals Stockholm ---------------------------------------------------------------------- From martin.norin@sto.pharmacia.se Wed Nov 8 10:32:18 1995 Received: from gatekeeper.pharmacia.se for martin.norin@sto.pharmacia.se by www.ccl.net (8.6.10/950822.1) id KAA04484; Wed, 8 Nov 1995 10:27:43 -0500 Received: from mailgate.pharmacia.se by gatekeeper.pharmacia.se; (5.65/1.1.8.2/16Feb95/sal) id AA03104; Wed, 8 Nov 1995 16:33:05 +0100 Received: by mailgate.pharmacia.se (5.65/DEC-Ultrix/4.3/sal-950131) id AA01677; Wed, 8 Nov 1995 16:23:12 +0100 Date: Wed, 8 Nov 1995 16:23:12 +0100 Received: from umc by mailgate.pharmacia.se via MR/PHAROS with conversational-MRIF; Wed, 08 Nov 95 16:23:11 +0100 Posted: Wed, 08 Nov 95 16:21:53 +0100 Sender: martin.norin@sto.pharmacia.se From: "NOYM" Message-Id: <1053211608111995/A03463/MEANIE> App-Message-Id: <1053211608111995/A03463/MEANIE/119B44153100> To: chemistry@www.ccl.net Subject: Summary Compressed PDB Lists Sensitivity: Company-Confidential Dear Colleagues, Thank you all for the replies to my question about a compressed pdb-list. They have been very useful for me. ===================================================================== The PDB directory currently consists of about 3800 records. However, many of these are different versions of the same structures (for example different mutants of the same protein or one protein with a number of different ligands or a lot of DNA/RNA structures). It would, for a number of reasons, be very valuable to have a subset of the PDB containing representatives ("the best structure") of each unique protein, and important conformers. If anybody have done a comprehensive investigation to compile such a list or if it is already available on the net please let me now ! I'm also interrested in any hints how to do this without manually going through every record in the PDB. ====================================================================== Here follows a summary: ====================================================================== CATH: You can also get similar information from our CATH web page, where Chris Orengo and Alex Michie have developed a hierarchical numbering system for related folds and sequences. I suggest starting with http://www.biochem.ucl.ac.uk/bsm/biocomp/index.html rob. ----|------ My comment: Take a look at this site if your into bioinformatics ! it contains structural classifications of proteins ( like in SCOP), algorithms for threading etc. ----|------ My comment again: Take also a look at the SCOP database (http:// scop.mrc-lmb.cam.ac.uk/scop/) ! ====================================================================== PDB_SELECT lists from the EMBL: Hi, It's been done by many people. Perhaps best by Sander's group at EMBL. You can get their latest PDB_SELECT lists from the EMBL file server (ftp.embl-heidelberg.de). A reference describing their method is Protein Science, 1, 409 ' 92. Hope this helps (or keeps you from redoing it yourself!), Jay Ponder, Washington Univ, St. Louis ====================================================================== DALI: Comparison of protein structures in 3D: I believe Chris Sander at EMBL has already done similar work (Hobohm & Sander, Protein Sci., 1994, 3:522-544) which should be accessible via the Net/Web at http://www.sander.embl-heidelberg.de. Good luck, Scott ----|------ My comment: This site should also be checked if your into bioinformatics: Below is a text I've extracted from the DALI web site (http://www.sander.embl-heidelberg.de). Here you also find a map of proein structure relations in a clustering diagram (look at the FSSP database): "The Dali server The Dali server is a network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank. A multiple alignment of structural neighbours is mailed back to you. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. If you want to know the structural neighbours of a protein already in the Protein Data Bank, you can find them in the FSSP database. You can ... submit coordinates by email (recommended) submit coordinates interactively (experimental) read a paper about the Dali method read a review about structure searches send feedback to the Dali authors get help with the Dali server retrieve precalculated structural similarities from the FSSP database look at 3D views of examples of unexpected structural similarities look at statistics about WEB access to Dali " ----|------ General comment: Comment from Max Vasquez, Several such compilations have been published by Chris Sander's group at the EMBL-Heidelberg (check their web site for an updated list) as well as by others (I happen to have a reference by Orengo and co-workers in Protein Engineering 6, 485 [1993]). Just be aware that these compilations tend to be more compressed that one may bargain for. For example, just one or very few serine proteases are included, similarly for immunoglobulins, etc. Best wishes, Max Vasquez, PhD, ===================================================================== Laura Walsh Annotated PDB File Listing: Suggested citations for use of this file are: L. L. Walsh, "Annotated PDB File Listing", Protein Science 1:5, Diskette Appendix (1992). She has broken down the PDB by molecule or compound. The latest revision I have of the listing is April 1994. Does anyone know of a more up to date listing? Jeff Nauss ----|------ My comment: Yes, the most updated list may be found in Lauras reply below. This list is very useful even now in the web-era. It contains a list of each molecule in alphabetic order with the resolution and other important information of each record in the PDB. The only drawback is that I have not found any more recent updates than from the Jan 94 release (see below for info of this release): ----|------ I did this a year ago last August. The results can be obtained from my www site: http://www.scs.uiuc.edu/~lwalsh A citation for a paper published about the process is included in the Work in Progress Annotation. Laura Walsh, ----|------ Also available at: Did you have a look at files in CCL archives in: /pub/chemistry/documents/PDB/PDB_file_list on www.ccl.net ? Jan jkl@ccl.net ====================================================================== Commercial: ...It is also only part of the story, in that there are also inconsistent atom labeling, so that searches for a given structure won't always find all of those hits. I don't know what public domain fixes there are, but I do know that Oxford Molecular went through the PDB database, making it consistent and fixing up irregularities. They now offer it as relational database called Iditis, so you should try contacting them. Their web page is at: http://www.oxmol.co.uk/ or I you could send email to: roger@madison.polytechnique.fr Good luck, Ernest Chamot, ----|------ Comment from Pieter Stouten: I always wondered why they would use a relational database paradigm. Proteins are ordered and the information one wants to retrieve often involves stretches of residues with certain characteristics. Using a relational database, one needs to do many operations. It seems to me that a mixture of pattern matching (with additional bonus of easily allowing for a few mismatches) and relational operations would be much more efficient. Does anybody have any opinions about this? Thanks, Pieter Stouten . ===================================================================== ---------------------------------------------------------------------- Martin Norin, Ph.D. e-mail:martin.norin@sto.pharmacia.se Dept. Struct. Biochem. Pharmacia Biopharmaceuticals Stockholm ---------------------------------------------------------------------- From owner-chemistry@ccl.net Wed Nov 8 11:17:18 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id LAA06515; Wed, 8 Nov 1995 11:15:46 -0500 Received: from goodyear.com for burkhart@goodyear.com by bedrock.ccl.net (8.7.1/950822.1) id LAA08005; Wed, 8 Nov 1995 11:15:43 -0500 (EST) Received: from rdsrv2 (rdsrv2.goodyear.com) by goodyear.com (4.1/SMI-4.1) id AA09134; Wed, 8 Nov 95 11:15:37 EST Received: from rds325 by rdsrv2 (4.1/SMI-4.1) id AA07251; Wed, 8 Nov 95 11:15:36 EST Received: by rds325 (931110.SGI/930416.SGI.AUTO) for chemistry@ccl.net id AA25236; Wed, 8 Nov 95 11:15:29 -0500 From: burkhart@goodyear.com (Craig W. Burkhart) Message-Id: <9511081115.ZM25234@rds325> Date: Wed, 8 Nov 1995 11:15:25 -0500 Organization: Goodyear Research X-Phones: (216)796-3163 Reply-To: cburkhart@goodyear.com X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: gamess-users@glue.umd.edu, chemistry@ccl.net Subject: GAMESS Front End Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Fellow Netters, I have been using GAMESS for some time now, and I was wondering what people were using as a GUI/builder/front end for it. I have been especially hampered in my use of GAMESS because of the difficulty of manual restarts. Going through the .dat file looking for $GRAD, $HESS and coordinate info, and then recasting the .inp file to account for the changes can be a bit labor-intensive. I would appreciate hearing how others in both the academic and corporate environs deal with automating their use of GAMESS. I will summarize the results to the list. Mucho thanks in advance... -- [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] Papernet: Craig W. Burkhart | The 1995 Cleveland Indians... Goodyear Research | 142 Goodyear Blvd | 1995 American League Central Akron, OH 44305 | Division Champions (100-44 .694) Mouthnet: 216.796.3163 | 1995 American League Champions (7-2) Faxnet: .3304 | [Next area under construction] Internet: cburkhart@goodyear.com | | The BEGINNING of a new baseball | dynasty. GO TRIBE...WORLD SERIES '96 | | AS FOR ART MODELL, SHAME & GOOD RIDDANCE. | DON'T SHOW YOUR FACE IN THIS TOWN AGAIN. [][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][][] From bschmitz@chm.uri.edu Wed Nov 8 12:17:19 1995 Received: from bach.chm.uri.edu for bschmitz@chm.uri.edu by www.ccl.net (8.6.10/950822.1) id MAA07551; Wed, 8 Nov 1995 12:08:48 -0500 From: Received: from chm.uri.edu by bach.chm.uri.edu via SMTP (950215.SGI.8.6.10/940406.SGI) for id MAA27431; Wed, 8 Nov 1995 12:08:41 -0500 Received: by chm.uri.edu (MX V4.0-1 VAX) id 1; Wed, 08 Nov 1995 12:08:59 EST Date: Wed, 08 Nov 1995 12:08:58 EST To: chemistry@www.ccl.net Message-ID: <0099915B.72436040.1@chm.uri.edu> Subject: superimposition Hello CCl, I am working on a new method for superimposing two molecules. I am trying to find numerical examples so that the various methods can be compared(molecules used, rms, time to superimpose , etc.). In addition, I am looking for information on a program called SUPERIMPOSE by K. Diederichs. Please respond to BSchmitz@chm.uri.edu. Thank you, Brian From owner-chemistry@ccl.net Wed Nov 8 12:47:20 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id MAA07976; Wed, 8 Nov 1995 12:37:24 -0500 Received: from saturn.kent.edu for raeker@saturn.kent.edu by bedrock.ccl.net (8.7.1/950822.1) id MAA08797; Wed, 8 Nov 1995 12:37:17 -0500 (EST) Received: by saturn.kent.edu (AIX 3.2/UCB 5.64/4.03) id AA16084; Wed, 8 Nov 1995 12:22:06 -0500 Date: Wed, 8 Nov 1995 12:22:06 -0500 (EST) From: "Todd J. Raeker" To: CCL Subject: pdb file generator Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello CCLer's Does anyone know of a program, free or commercial that will create a pdb file given the amino acid sequence. Either a MS Windows or UNIX program would be great to have. A graphical display is not required. Thanks, Todd. Dr. Todd J. Raeker | Department of Chemistry raeker@saturn.kent.edu | Kent State University Phone (216)-672-2986 | Kent, OH 44242-0001 From owner-chemistry@ccl.net Wed Nov 8 13:02:19 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id MAA07920; Wed, 8 Nov 1995 12:35:14 -0500 Received: from uscmail.usc.es for qftramos@usc.es by bedrock.ccl.net (8.7.1/950822.1) id MAA08750; Wed, 8 Nov 1995 12:34:24 -0500 (EST) Received: by uscmail.usc.es (5.67b/1.34) id AA20783; Wed, 8 Nov 1995 18:34:34 +0100 Date: Wed, 8 Nov 1995 18:34:34 +0100 (MET) From: Antonio Fernandez Ramos To: chemistry@ccl.net Subject: FIT & REPRESENT potential function Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters, I am trying to develop some potential function for several dimers to further use the functions obtained in simulations in condensed phase. I have done explorations of the potential surface, but now I have some problems to fit the results to a function. I would need, if possible, some fortran code to fit the results (preferably using first and second derivatives of the function) and a code to optimize the function with some constrains, in order to obtain some isoenergetic relaxed contour maps, and check the orientational behavior of the potential. From ccl@cric.chemres.hu Wed Nov 8 14:17:20 1995 Received: from cric.chemres.hu for ccl@cric.chemres.hu by www.ccl.net (8.6.10/950822.1) id OAA09775; Wed, 8 Nov 1995 14:07:01 -0500 From: Received: by cric.chemres.hu (AIX 3.2/UCB 5.64/4.03) id AA23018; Wed, 8 Nov 1995 20:00:30 +0100 Date: Wed, 8 Nov 1995 20:00:30 +0100 (NFT) To: "Vernon G. Box" Cc: system@alchemy.chem.utoronto.ca, CHEMISTRY@www.ccl.net, mayer@cric.chemres.hu Subject: Re: CCL:BOND ORDERS In-Reply-To: <9511012002.AA09433@scisun.sci.ccny.cuny.edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 1 Nov 1995, Vernon G. Box wrote: > Hi All > > What is the significance of a "negative" bond order? Is it simply > an expression of the presence of an anti-bond or no bond? > > VB > The question is not trivial. As far as I remember, one cannot produce negative bond orders in any two electron - two basis orbitals problem. Moreover, filling twice either a bonding or an antibonding orbital will give a bond order of one, while filling both we get zero - provided that the bonding and antibonding orbitals are composed of the same hybrids, and differ only by their signs (and normalization constant). Negative bond order between two atoms can, therefore, be obtained if there are interferences from different bonding and antibonding contributions. One should also take into account that no negative bond orders are possible in an orthogonalized basis - then the bond order reduces to the Wiberg index which represent a sum of squares. So negative mond orders are a subbtle overlap effect. Yours sincerely, Prof. Istvan Mayer Please use e-mails: mayer@cric.chemres.hu IB13LVIB@HUEARN.sztaki.hu H1376May@ella.hu Central Research Institute for Chemistry of the Hungarian Academy of Sciences H-1525 Budapest, P.O.Box 17 Hungary From owner-chemistry@ccl.net Wed Nov 8 15:02:21 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id OAA10758; Wed, 8 Nov 1995 14:53:39 -0500 Received: from olimp.irb.hr for kiralj@olimp.irb.hr by bedrock.ccl.net (8.7.1/950822.1) id OAA10216; Wed, 8 Nov 1995 14:50:25 -0500 (EST) From: Received: by olimp.irb.hr (MX V4.1 VAX) id 37; Wed, 08 Nov 1995 20:49:10 MET-DST Date: Wed, 08 Nov 1995 20:49:09 MET-DST To: CHEMISTRY@ccl.net Message-ID: <009991A4.1DB11894.37@olimp.irb.hr> Subject: summary of the pi stacking area calculation Dear CCL Netters, here is the summary about the pi stacking area calculation. Those interested generally in pi stacking calculations can find an older CCL summary by Mirko Kranenburg on 21 Jul 1995 (e-mail:mirko@SARA.NL). -------------------------------------------------- My question: ------------ Dear CCL Netters, Does anybody know for some program applicable to crystals or molecules with pi stacking interactions, that calculate area of the aromatic molecule or fragment covered by the neighbour aromatic molecule or fragment? I shall summarize the replies. Thanks in advance. Rudolf ------------- Rudolf Kiralj Department of Materials Science and Electronics Rudjer Boskovic Institute Bijenicka 54 10 000 Zagreb Croatia e-mail: kiralj@olimp.irb.hr Replies: -------- 1) Dear Rudolf, I'm interested to know what sort of calculations you're doing involving pi-stacking interactions. I will presently be studying the packing of conducting polymer chains after I build and optimise some oligomer molecules of polyaniline with AM1. The pi-interactions will have to be taken into account. Maybe you may have some expertise or ideas in this area ? Keep in touch.> : Dr. Aidan Boyle Instituto de Quimica UNICAMP CP 6154 13.081-970 Campinas SP Brazil Tel: 00-55-192-397266 Fax: 00-55-192-393805 e-mail: BOYLE@IQM.UNICAMP.BR 2) Dear Dr. Rudolf Kiralj Could you please tell me if you got any responses to your query? Thanks for your help pavan please send your mail to pavan@bnpi.com 3) Please send me a copy of responses you receive for pi-stacking /area// Thanks in advance Satyam SATYAM@vms.cis.pitt.edu 4) Dear Rudolf, When you summarize the CCL replies, could you join some bibliographic references about pi stacking interactions? Thanks in advance, Nathalie meurice@scf.fundp.ac.be My repeated question: -------------------- Dear CCL Netters, Last week I posted to the CCL inquiring with the following problem: Does anybody know for some program applicable to crystals or molecules with pi stacking interactions, that calculate area of the aromatic molecule or fragment covered by the neighbour aromatic molecule or fragment? Since I have no answers to summarize the subject, and supposing my question was not precise enough, I am asking for help on the pi stacking area calculations: Suppose one have several solved crystal structures or extracted from Cambridge Structural Database, or molecules are built and optimized by molecular mechanics or quantum mechanics programs. If these molecules are partially or completely aromatic, then it is possible that neighbour molecules or aromatic fragments are mutually parallel and on the distance approximately 3.5 A. If one can find a suitable view normal to the aromatic planes, stacking could be observed as covering of one aromatic system by one or two neighbour system. By changing the relative positional parameters of the neighbour aromatic systems this covering is changed. In the first approximation it could be taken that measure of this covering is area of the observed aromatic system (the system is taken as planar hexagons) or surface area (the system is supposed to be three-dimensional in pi interactions, and the interacting surface is not a plane containing the hexagons). The question is: Is there any program or appropriate reference dealing with such or similar calculations of the covering (pi stacking) areas or surface areas for a specified set of relative positional parameters? Any information or suggestion is welcome. Thanks in advance. Rudolf ------------- Rudolf Kiralj Department of Materials Science and Electronics Rudjer Boskovic Institute Bijenicka 54 10 000 Zagreb Croatia e-mail: kiralj@olimp.irb.hr Replies: -------- 1) Rudolf, I have also wondered about the quantitative treatment of pi stacking interactions. But I have no info/references on it. I would be interested to hear from someone who could shed some light on the topic. Jeanne *************************************** Jeanne Siemion, MS Academic Computing Services Advanced Technology Laboratory for Molecular Development Enrico Fermi Institute 5640 S. Ellis Ave. U of Chicago, Chicago, IL, USA phone: 312-702-7825 fax: 312-702-8038 e-mail: siemion@rainbow.uchicago.edu office: EFI 184 *************************************** 2) I have a program designed primarily to look at steric effects in terms of cone angles and solid angles in organometallics, but which has been expanded to include molecular volumes in crystals. I am now adding a feature to calculate the area of a molecules projection onto a plane analytically. It would not be very difficult to enhance this to include the area of overlap of two molecules onto that plane, which seems to be what you are after (at least one possible solution). The resulting calculation would do several things: - find the l.s. plane through predefined groups of atoms (eg. phenyl groups) - projection all atoms, or selected atoms, onto plane - calculate the area of that region due to projection of atoms from two groups of interest. If this is what you are interested in, I'm sure I could add the calculation after I've completed the normal molecular projection area code. 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 craig@hobbes.gh.wits.ac.za From walterse@mis.finchcms.edu Wed Nov 8 15:17:24 1995 Received: from mis.finchcms.edu for walterse@mis.finchcms.edu by www.ccl.net (8.6.10/950822.1) id PAA11310; Wed, 8 Nov 1995 15:07:35 -0500 Received: from [192.217.124.142] by mis.finchcms.edu; (5.65/1.1.8.2/05May95-1218PM) id AA21702; Wed, 8 Nov 1995 14:07:12 -0600 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Date: Wed, 8 Nov 1995 14:07:32 -0600 To: CHEMISTRY@www.ccl.net From: walterse@mis.finchcms.edu (Dr. Eric Walters) Subject: 3D databases--summary Some time ago I sent the following question to the list. Attached is a summary of replies. Thanks to all who contributed! >I am looking for 3D structure databases which are accessible [read: >inexpensive] for academic users. A search of the CCL archives indicates >the question has been asked before, but not very satisfactorily answered. > >What are the choices? What do they cost? How good are they? Thanks for >your input--I will summarize replies to the list. --------------- =46rom: MARTIN@cmda.abbott.com The NCI database is the only one I know of. Yvonne -------------- =46rom: toni@athe.wustl.edu (Toni Kazic) Eric, for proteins: http://pdb.pdb.bnl.gov/ for nucleic acids: http://ndbserver.rutgers.edu:80/ for small molecules: http://ibc.wustl.edu/klotho/ PDB and NDB are pretty complete I think. Klotho has 439 compounds of quasi-minimized energy. All are free. I know of no others. Toni Kazic -------------- =46rom: Dan Zaharevitz 301-496-8747 If you are looking for 3D database searching software; I don't think there are any free programs out there. I think all the commercial vendors ( Chem Design, MDL, Tripos, etc. ) offer some kind of academic discount, but that makes their product less expensive, not necessarily inexpensive. If you are looking for just the databases, then you might be interested in structures the NCI has made available. There are several possibilities for obtaining structural infomation from NCI. There is a set of about 125,000 connection tables in MDL's MACCS format. This set is available via anonymous ftp from helix.nih.gov anonymous ftp to helix.nih.gov cd ncidata/2D In this directory there should be 3 files including a .readme file. The connection table file is compressed with the standard UNIX compress. It takes up about 11 Meg compressed and expands to about 190 Meg. This file contains only the connection table, no coordinates ( 2D or 3D ) are available. The Gasteiger group has used Corina to do the 2D to 3D conversion for these structures and they are also available via anonymous ftp from helix ( directory ncidata/3D ). Again, this data is available as MACCS format sd files and is not searchable in any sensible way without database software. If you don't want to build a database from connection tables, you should contact the vendor of your database software. All the companies I know of have built a database with them. The NCI has had no involvement in these database builds and also has no control of how much money the companies charge for providing the database. As far as I know all the companies are offering this database free to their customers, although I have heard reports that some don't tell you of its availability or price unless you ask. At the NCI we have used Chem-X from Chemical Design to build databases from connection tables. Details have been published: Milne, et. al. J. Chem. Info. Comput. Sci. 34:1219-1224(1994) There is also a WWW page that contains very detailed information on how we build and search databases. The URL is: http://www.ncifcrf.gov:1994/DTP/dis3d.html We are very close ( a few weeks or so ) to releasing results from the cancer and AIDS screening programs for about 30,000 compounds. These results will also be available via anonymous ftp and I'm sure the various database vendors will pick it up and repackage it for their particular system. If you have any questions feel free to contact me. DanZ. /********************************************************************** * Dan Zaharevitz * Information Technology Branch, Developmental Therapeutics Program * National Cancer Institute * EPN Room 811, 6130 Executive Blvd. Rockville, MD 20892-9903 * email: zaharevitz@dtpax2.ncifcrf.gov phone: (301)496-8747 **********************************************************************/ ---------- =46rom: "Dimitris Agrafiotis" NCI maintains a 3D database with over 100,000 structures in it. You can get it via anonymous ftp, but I can't remember the name of the site. Contact Dan Zaharevitz at "zaharevitz@dtpvx2.ncifcrf.gov" for more details. Cheers, -- Dimitris K. Agrafiotis, PhD | e-mail: dimitris@3dp.com Principal Research Scientist | tel: (610) 458-6045 3-Dimensional Pharmaceuticals, Inc. | fax: (610) 458-8249 665 Stockton Drive, Suite 104 Exton, PA 19341 --------------- =46rom: Erich Bornberg-Bauer eric, depends on what inexpensive is and what kind of data you need. for proteins it's the pdb - database (further info upon request) else for biopolymers you may look at the embl - server erich +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Erich Bornberg - Bauer, PhD Institut fuer Mathematik, Abteilung Computerorientierte Mathematik A-1090 Strudlhofg. 4, Tel.: *43-1-407 63 63, erich@cma.univie.ac.at and Institut fuer Theoretische Chemie, Abteilung Theoretische Biochemie A-1090 Waehringerstr. 17 / 4, e-mail: erich@tbi.univie.ac.at Tel.: *43 - 1 - 40 480 - 667, 677 Fax.: *43 - 1 - 402 85 25 University Vienna / Austria ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ --------------- =46rom: "=03)" The Cambridge Structural Database is the obvious choice. I think they give academic discounts, but I'm not sure of the costs involved. ------------------------------------------------------------ Prof. Helder M. Marques, Department of Chemistry University of the Witwatersrand, P.O. Wits 2050 Johannesburg, South Africa =46ax: Int + 27 + 11 + 339-7967 ------------------------------------------------------------ =46rom: Craig Taverner I use the Cambridge Structural Database. I think, though, that it is quite expensive to purchase the licence, although with the advent of linux (PC unix) it is no longer expensive to run. Contact Frank Allen (allen@chemcrys.cam.ac.uk) for details. 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 ----------------- =46rom: Computational Chemistry To: walterse@mis.finchcms.edu Subject: Re: Re: CCL:looking for 3D databases =46orwarding: Mail from '' dated: Wed, 20 Sep 1995 18:09:11 +0200 ---------- Begin Forwarded Message ---------- =46rom Claude.C.LUTTMANN@VITRY.RPR/RD/CRVA/CHIMIE.RP-RORER.rp.fr Dear Eric, I know one 3D database that is very inexpensive i.e. free of charge ! That i= s the NCI3D database (National Cancer Institut). It seems to me that it is sol= d not as a database but as an SD file (not connected to a specific database sofware). The 2D structures have been converted by the 2D/3D conversion prog= ram CORINA. As far as I have seen the 3D structures are very good (CORINA is an excellent conversion program). This database contains over 120 000 3D structures. MDL is a sofware company that is well known in information systems for chemi= cal and pharmaceutical industry and sells a number of 3D databases but these may= be quite expensive and you need a license for their sofware. Tripos and Chemica= l Design (UK) are companies that sell a lot of 3D databases too but these are = in a format that is directly related to their database modules. So, in addition= to the databases, you have also to buy the necessary software. In total this ma= y become quite expensive. Hope this helps Best regards, **************************************************************************** * Dr C. LUTTMANN * Rhone-Poulec RORER S.A. * Centre de recherches de Vitry-Alfortville * 13, quai jules Guesde B.P.14 * 94403 Vitry-sur-Seine - Paris - France * Tel +1-45-73-78-30 Fax : +-1-45-73-80-14 Email: LUTTMANN@RP.FR **************************************************************************** ------------- =46rom: WCUI@mbcl.rutgers.edu 3D database for proteins : Brookhaven Protein Databank. for small molecules : Cambridge Crystal Database. (Cambridge U.) -------------- =46rom: "Osman F. G=FCner" Eric: In response to your question on 3D databases, I am sure that you are familia= r with MDL databases. In a nut shell: ACD-3D is a database of commercially available chemicals; by analogy, it is the electronic version of 200+ chemical catalogs; contains 153,000 3= D structures MDDR-3D compounds that are patented for a certain therapeutic category, base= d on Prous' "Drug Data Report" contains 57,000 3D structures CMC-3D is a database of drugs in the marketplace; based on Pergamon's six volume "Comprehensive Medicinal Chemistry"; contains 6,200 3D structures. NCI-3D is a database of non-proprietary compounds that are submitted to NCI = for screening; contains 125,000 3D structures There is a fee for the use of the first three databases; the last one is for free. Please let me know if you would like more information about these databases. Cheers...Osman ------------------------------------------------- Osman F. Guner, PhD, -- Senior Scientist MDL Information Systems, Inc. -- (510) 895-1313 San Leandro, CA 94577, U.S.A. -- Osman@mdli.com ---------------- =46rom: Weifan Zheng You can download NCI 3D database for 125,000 compounds for your test. ftp helix.nih.gov login: anonymous password: your email address cd ncidata/3D If you get any other useful info, please let me know. Thanks! Weifan Zheng, Lab for Molecular Modeling School of Pharmacy UNC-Chapel Hill NC 27599-7360 ------------- * D. Eric Walters, Ph.D., Associate Professor, Biological Chemistry * Finch University of Health Sciences/The Chicago Medical School * 3333 Green Bay Road, North Chicago, IL 60064 * ph 708-578-8613;fax 708-578-3240; email: walterse@mis.finchcms.edu * "A man would do nothing if he waited until he could do it so well that * no one would find fault with what he had done." --Cardinal Newman * ***** note new phone number! ***** From laaksone@csc.fi Wed Nov 8 15:47:23 1995 Received: from finsun.csc.fi for laaksone@csc.fi by www.ccl.net (8.6.10/950822.1) id PAA12198; Wed, 8 Nov 1995 15:38:24 -0500 Received: (from laaksone@localhost) by finsun.csc.fi (8.6.9/8.6.9+CSC-2.0) id WAA20882; Wed, 8 Nov 1995 22:38:23 +0200 Content-Transfer-Encoding: 8bit Date: Wed, 8 Nov 1995 22:38:23 +0200 (EET) From: Leif Laaksonen Subject: SYBYL binary trajectory file format To: chemistry@www.ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Computational Chemists, I'm sorry to bug the whole list again, but knowing how useful this list is I can resist the temptation... Is there anybody out there who knows the SYBYL md binary trajectory file format? I need the format for my own analysis program but I can't find the information. This is almost as tricky to solve as the X-PLOR equivalence has proved to be... Please reply to me directly! I will summarize the stuff (if needed). 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---------- Tried to save the trees. Bought a plastic bag. The bottom fell out. It was a piece of crap. N. Young ------------------------------------------------------------------- From olsonl@darwin.pprd.abbott.com Wed Nov 8 16:47:25 1995 Received: from abtlabs.pprd.abbott.com for olsonl@darwin.pprd.abbott.com by www.ccl.net (8.6.10/950822.1) id QAA13775; Wed, 8 Nov 1995 16:43:34 -0500 Received: from darwin.pprd.abbott.com by abtlabs.pprd.abbott.com with SMTP id AA09333 (5.65c/IDA-1.4.4 for ); Wed, 8 Nov 1995 15:43:33 -0600 Received: by darwin.pprd.abbott.com (940816.SGI.8.6.9/930416.SGI) for CHEMISTRY@www.ccl.net id PAA12307; Wed, 8 Nov 1995 15:57:02 -0600 Date: Wed, 8 Nov 1995 15:57:02 -0600 From: olsonl@darwin.pprd.abbott.com (Leif P. Olson) Message-Id: <199511082157.PAA12307@darwin.pprd.abbott.com> To: CHEMISTRY@www.ccl.net Subject: PM3 summary Greetings CCLers, Last week I asked the question: >A referee for a paper I submitted states that "PM3 is well-known to >overestimate proton barrier heights". He/she may be right (although >this has no effect on the conclusions in the paper), but in any case >I need to find a specific reference which addresses this "well-known" >fact. I would appreciate it if someone could point me to such a >reference. > >Thank you. Of course I should have specified proton *transfer* barrier heights. Opinion was unanimous: the referee was right. Here are the replies that I received, which directed me to several very nice papers... ************************************************************************** Hmmmm... I'm not sure of a specific reference, but that does seem correct. I know that MNDO does this. I can point you to a reference where this was documented and you can take it from there. Bofill, J. M.; Castells, J.; Olivella, S.; Sole, A. J. Org. Chem. 1988, 53, 5148. Hope that this helps. Best regards, Andy Holder =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER President Semichem, Inc. || Internet Addr: aholder@cctr.umkc.edu 7128 Summit || Phone Number: (913) 268-3271 Shawnee, KS, 66216 || FAX Number: (913) 268-3445 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= *************************************************************************** Yes. It's true that semiempirical molecular orbital methods such as AM1 and PM3 tend to overestimate barrier involving proton transfer. The most obvious reason is that the heat of formation for proton is off by very large amount, so it affects the transition state too. I do not have any specifc reference other than my own. Zheng, Y.-J.; Merz, K. M., Jr.; Farber, G. K. Protein Engineering 1993, 6 , 479-484. Hope this is useful. Yajun **************************************************************************** I think that the referee is right. Unfortunately I do not know references about that problem, but my own work shows (J. Comput. Chem. 13, 860-866, 1992) that PM3 barriers for proton transfer are up to 300 % higher than ab initio/experimental values. All the standard semiempirical methods are practically useless to describe accurately the hydrogen bonds. Both geometry and barriers are bad described with MNDO, AM1 or PM3. PM3 is better for geometries, but is worse than AM1 for barriers. Only the modified semiempirical methods seem to provide a way to solve the hydrogen bond topic. Best regards Jesus Rodriguez Departamento de Quimica Fisica Facultad de Quimica, Universidad de Santiago 15706 Santiago de Compostela, SPAIN e-mail: qftjesus@usc.es ***************************************************************************** Thanks to the respondents for solving my problem. These references will definitely be added to the paper. Leif Olson, Ph.D. olsonl@darwin.pprd.abbott.com Department of Structural Biology Abbott Laboratories Abbott Park, IL From tj@eecs.uic.edu Wed Nov 8 17:17:24 1995 Received: from mail.eecs.uic.edu for tj@eecs.uic.edu by www.ccl.net (8.6.10/950822.1) id RAA14335; Wed, 8 Nov 1995 17:08:04 -0500 Received: from bert.eecs.uic.edu (bert.eecs.uic.edu [128.248.166.23]) by mail.eecs.uic.edu (8.6.11/8.6.10) with ESMTP id QAA19710 for ; Wed, 8 Nov 1995 16:08:05 -0600 From: tj ODonnell Received: (tj@localhost) by bert.eecs.uic.edu (8.6.10/8.6.10) id QAA27174 for chemistry@www.ccl.net; Wed, 8 Nov 1995 16:08:22 -0600 Message-Id: <199511082208.QAA27174@bert.eecs.uic.edu> Subject: structure of d4T To: chemistry@www.ccl.net (CCL) Date: Wed, 8 Nov 1995 16:08:21 -0600 (CST) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 900 The NY Times and Chicago Tribune reported today about the FDA approval of 3TC. They didn't even give the (equally obscure) names lamivudine or epivir. I guess its too much to ask that they give a proper chemical name, much less a structure. Well, I found 3TC=lamivudine=epivir easily enough, but they made mention of d4T. I have not found any reference to a compound by this name, yet I have seen this name used before. Can anyone help me with synonyms, proper chemical names, or best a real structure (2D or 3D) of d4T? Thanks, TJ -- *---------------------------------------------------------------------* * If you need a quote: http://www.eecs.uic.edu/~tj/quotes.html * *---------------------------------------------------------------------* | Dr. TJ O'Donnell > tj@eecs.uic.edu < http://www.eecs.uic.edu/~tj/ | *---------------------------------------------------------------------* From /G=Matthew/S=Harbowy/OU=LIPTONUS-EC02/O=TMUS.TJL/@LANGATE.gb.sprint.com Wed Nov 8 18:17:26 1995 Received: from reston-mx1.telemail.net for /G=Matthew/S=Harbowy/OU=LIPTONUS-EC02/O=TMUS.TJL/@LANGATE.gb.sprint.com by www.ccl.net (8.6.10/950822.1) id SAA15592; Wed, 8 Nov 1995 18:13:38 -0500 From: X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Wed, 8 Nov 1995 15:06:00 -0500 X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Wed, 8 Nov 1995 15:06:00 -0500 X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Wed, 8 Nov 1995 15:06:00 -0500 X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Wed, 8 Nov 1995 15:06:00 -0500 Date: Wed, 8 Nov 1995 15:06:00 -0500 X400-Originator: /G=Matthew/S=Harbowy/OU=LIPTONUS-EC02/O=TMUS.TJL/@LANGATE.gb.sprint.com X400-Recipients: non-disclosure:; X400-MTS-Identifier: [/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/;Wed Nov 8 15:06:37 199500] X400-Content-Type: P2-1984 (2) Content-Identifier: Re: CCL:Global m Message-ID: <"Wed Nov 8 15:06:37 199500*/G=Matthew/S=Harbowy/OU=LIPTONUS-EC02/O=TMUS.TJL/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/"@MHS> Cc: chemistry@www.ccl.net Subject: Re: CCL:Global minimum (philosophical) problems... It is not always desired to reach the global minimum. One needs to understand what geometries are realistic and applicable to experimental problems. It is not necessarily the case that a protein will be formed in its global minimum: it my have been formed into a specific conformation and the barrier to transition is too high to permit movement into the minimum. Also, the arrangement of atoms may be arranged into a lower energy state, but obviously one does not want to break chemical bonds during minimization. Or, you may be interested in the properties of cis-butane or boat-cyclohexane, whose conformations we know and can reach. It would seem, philosophically, that the search for global minima of massive proteins does not have a demonstrated value-added application as yet. matt From demos@home.amug.org Wed Nov 8 19:32:25 1995 Received: from home.amug.org for demos@home.amug.org by www.ccl.net (8.6.10/950822.1) id TAA16318; Wed, 8 Nov 1995 19:28:35 -0500 Received: from [128.110.196.225] by home.amug.org via SMTP (940816.SGI.8.6.9/940406.SGI.AUTO) for id QAA04750; Wed, 8 Nov 1995 16:29:22 -0800 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 8 Nov 1995 06:32:57 +0100 To: chemistry@www.ccl.net From: demos@home.amug.org (Dmitry Boldyrev) Subject: MolDes for Macintosh Hi all! I just joined the list. Looks nice, but needs more advertising. I am author of Molecule Designer (which actually never made it to its destination) available on info-mac. I heard about MacSpartan and that made me curious. Does anyone here have anything to do with SPARTAN? If I can be helpful with any advise on mac programming, I am willing to help for free! I am quite experienced Mac programmer. Please let me know! Also, question rises if anyone here is interested to see development of MolDes? Last thing I want to mention is next ACTC meeting which will be held in Park City (UTAH) coming summer. If you'd like to find out more, cruise over to http://amug.org/~demos/actc/actc.html. Thanks for your time reading this article. Demos Author of MolDes, PowerIRC, PowerTCP, StarGate, DemoBot, Spectra, LZSS Res. ___________________________________________________________________ Demos | IRC: #macdev | http://amug.org/~demos From owner-chemistry@ccl.net Wed Nov 8 21:32:26 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id VAA17779; Wed, 8 Nov 1995 21:22:46 -0500 Received: from camsci.com for jsb2@camsci.com by bedrock.ccl.net (8.7.1/950822.1) id VAA13956; Wed, 8 Nov 1995 21:22:41 -0500 (EST) From: Date: Wed, 8 Nov 95 21:22:38 EST Received: by camsci.com (4.1/3.1.090690-Cambridge Scientific Computing) id AA25621; Wed, 8 Nov 95 21:22:38 EST Message-Id: <9511090222.AA25621@camsci.com> To: chemistry@ccl.net, raeker@saturn.kent.edu Subject: Re: CCL:pdb file generator > Does anyone know of a program, free or commercial that will create a >pdb file given the amino acid sequence. Either a MS Windows or UNIX >program would be great to have. A graphical display is not required. CS Chem3D Pro (available for Windows and Macintosh, but not UNIX) will do this, depending on what you want to do. That is, it can take an amino acid sequence and output a file in PDB format that represents one possible configuration of that protein, but anything relating to secondary or tertiary structure is pulled out of mostly-thin air. The current C&E News has a nice article about two programs that attempt to predict secondary and tertiary protein structures. More information (about Chem3D, not C&E News) is available at http://www.camsci.com The ACS has been pretty good about putting computer-related articles on http://pubs.acs.org, but this week's article isn't there at the moment. Jonathan Brecher CambridgeSoft Corporation jsb@camsci.com