From chemistry-request@server.ccl.net Mon May 20 02:55:24 2002 Received: from cuces.unisi.it ([193.205.4.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4K6tN124120 for ; Mon, 20 May 2002 02:55:23 -0400 Received: from CONVERSION-DAEMON.unisi.it by unisi.it (PMDF V6.0-24 #43309) id <01KHY14AWPLS004RXA@unisi.it> for chemistry@ccl.net; Mon, 20 May 2002 08:55:22 +0100 (MET) Received: from unisi.it (ccmaol3.chim.unisi.it [192.167.123.208]) by unisi.it (PMDF V6.0-24 #43309) with ESMTPA id <01KHY14A2E0U004QTG@unisi.it>; Mon, 20 May 2002 08:55:21 +0100 (MET) Date: Mon, 20 May 2002 08:55:31 +0200 From: "Nicolas Ferre'" Subject: Re: CCL:Re:g98 Symmetry Sender: ferre@unisi.it To: Roma Oakes Cc: chemistry@ccl.net Message-id: <3CE89DE3.E773E26F@unisi.it> Organization: Universita` di Siena MIME-version: 1.0 X-Mailer: Mozilla 4.61i [en_US] (X11; I; AIX 4.3) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT X-Accept-Language: fr, en References: Hi Roma, One or two years ago, there was already a discussion on CCL about this problem. Actually G98 cannot deal with "increasing" symmetry(C2 -> D2 in your case), due to memory problems, i.e. when the symmetry becomes higher, you need more space to save some useful informations than what is allocated at the start of your calculation (lower symmetry). A quick fix is possible (link 202) if you have the source code ... Nicolas Roma Oakes wrote: > > Dear All > > thanks to all who responded to my question about symmetry in G98. I have > been sent a few files, some with C2 symmetry and one with D2, I'll be trying > them all, but they have certainly helped a lot. Mind you, one of the jobs > (that had started with C2 symmetry) had been going along very well when it > crashed with; (I had used iop(2/17=1, 2/16=3) > > Leave Link 103 at Sun May 19 17:48:29 2002, MaxMem= 73400320 cpu: > 51.0 > (Enter C:\G98W\l202.exe) > Stoichiometry C36H46N4 > Framework group D2[C2'(N.N),C2"(NH.HN),X(C36H44)] > Deg. of freedom 63 > Full point group D2 NOp 4 > Omega: Change in point group or standard orientation. > > Largest Abelian subgroup D2 NOp 4 > Largest concise Abelian subgroup D2 NOp 4 > Operation on file out of range. > FileIO: IOper= 1 IFilNo(1)= -579 Len= 172 IPos= 0 Q= > 56304400 > > (a lot of stuff about dumping files) > > Number 0 > Base 20480 > End 66048 > End1 66048 > Wr Pntr 20480 > Rd Pntr 20480 > Error termination in NtrErr: > NtrErr Called from FileIO. > > I've restarted it but don't really know what the error means > > Regards Roma > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nicolas FERRE' (PhD) phone/fax : +39-0577-234278 Dipartimento di Chimica Universita` di Siena mailto:ferre@unisi.it via Aldo Moro 53100 SIENA (Italia) http://ccmaol1.chim.unisi.it/ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Mon May 20 03:42:51 2002 Received: from thor.chem.sdu.dk ([130.225.142.15]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4K7go125359 for ; Mon, 20 May 2002 03:42:50 -0400 Received: from localhost (tetz@localhost) by thor.chem.sdu.dk (SGI-8.9.3/8.9.3) with ESMTP id JAA83886; Mon, 20 May 2002 09:45:25 +0200 (MDT) Date: Mon, 20 May 2002 09:45:25 +0200 From: Per Tetzschner Olsen To: Roma Oakes cc: ccl Subject: Re: CCL:Re:g98 Symmetry In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Roma It seems to me that you have a change of point group, which causes some minor problems in G98. You can avoid this with iop(2/16=1)... hope this helps. Per On Sun, 19 May 2002, Roma Oakes wrote: > Dear All > > thanks to all who responded to my question about symmetry in G98. I have > been sent a few files, some with C2 symmetry and one with D2, I'll be trying > them all, but they have certainly helped a lot. Mind you, one of the jobs > (that had started with C2 symmetry) had been going along very well when it > crashed with; (I had used iop(2/17=1, 2/16=3) > > Leave Link 103 at Sun May 19 17:48:29 2002, MaxMem= 73400320 cpu: > 51.0 > (Enter C:\G98W\l202.exe) > Stoichiometry C36H46N4 > Framework group D2[C2'(N.N),C2"(NH.HN),X(C36H44)] > Deg. of freedom 63 > Full point group D2 NOp 4 > Omega: Change in point group or standard orientation. > > Largest Abelian subgroup D2 NOp 4 > Largest concise Abelian subgroup D2 NOp 4 > Operation on file out of range. > FileIO: IOper= 1 IFilNo(1)= -579 Len= 172 IPos= 0 Q= > 56304400 > > > (a lot of stuff about dumping files) > > Number 0 > Base 20480 > End 66048 > End1 66048 > Wr Pntr 20480 > Rd Pntr 20480 > Error termination in NtrErr: > NtrErr Called from FileIO. > > I've restarted it but don't really know what the error means > > Regards Roma > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Mon May 20 04:21:52 2002 Received: from alpha.si.unimib.it ([149.132.2.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4K8Lq125984 for ; Mon, 20 May 2002 04:21:52 -0400 Received: from apandini.disat.unimib.it ([149.132.36.68]) by alpha.si.unimib.it (Post.Office MTA v3.5.3 release 223 ID# 1007-71762U2500L200S0V35) with ESMTP id it for ; Mon, 20 May 2002 10:21:43 +0200 Date: Mon, 20 May 2002 10:24:45 +0200 From: alessandro.pandini@unimib.it (Pandini Alessandro - Dottorati di Ricerca) To: chemistry@ccl.net Subject: Protein structure resolution and MD equilibration Message-ID: <20020520082445.GA16508@apandini.disat.unimib.it> Reply-To: alessandro.pandini@unimib.it Mime-Version: 1.0 Content-Type: text/plain; format=flowed; charset=ISO-8859-15 Content-Disposition: inline Content-Transfer-Encoding: 8bit X-Mailer: Balsa 1.3.5 Lines: 13 Dear all, I'm looking for good references on this topic: relationships between crystal structure resolution of proteins and equilibration timescale in Molecular Dynamics. Does anyone know any recent study? I'll summarise. Thanks Alex From chemistry-request@server.ccl.net Mon May 20 08:53:24 2002 Received: from ns1.tudelft.nl ([130.161.180.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4KCrO129650 for ; Mon, 20 May 2002 08:53:24 -0400 Received: from CONVERSION-DAEMON.mailhost2.tudelft.nl by mailhost2.tudelft.nl (PMDF V6.0-025 #40925) id <0GWE00G01UGQGW@mailhost2.tudelft.nl> for chemistry@ccl.net; Mon, 20 May 2002 14:53:16 +0200 (MEST) Received: from listserv.tudelft.nl (listserv.tudelft.nl [130.161.180.33]) by mailhost2.tudelft.nl (PMDF V6.0-025 #40925) with ESMTP id <0GWE009LWUGQAX@mailhost2.tudelft.nl> for chemistry@ccl.net; Mon, 20 May 2002 14:53:14 +0200 (MEST) Received: from stm-ltc2.dct.tudelft.nl (stm-ltc2.dct.tudelft.nl [130.161.196.198]) by listserv.tudelft.nl (8.10.2+Sun/8.10.2) with ESMTP id g4KCrD316257 for ; Mon, 20 May 2002 14:53:14 +0200 (MEST) Received: from STM-LTC2/SpoolDir by stm-ltc2.dct.tudelft.nl (Mercury 1.47) ; Mon, 20 May 2002 14:53:14 +0000 (MET-1MEST) Received: from SpoolDir by STM-LTC2 (Mercury 1.47); Mon, 20 May 2002 14:53:12 +0000 (MET-1MEST) Date: Mon, 20 May 2002 14:53:03 +0200 From: Martijn Zwijnenburg Subject: bond lenghts To: chemistry@ccl.net Message-id: <3CE90DBE.19813.4314342A@localhost> MIME-version: 1.0 X-Mailer: Pegasus Mail for Win32 (v3.12c) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Priority: normal Hi, I'm looking for a program which can read in the structure of a molecule (as pdb or xyz) and output a table of bond-lengths (or atom-atom distances for what it's worth). No difficult analysis methods needed, just one structure. I'm thinking of an output like: Si1-O4 1.644 Si1-O5 1.643 etc. etc. I can do this by hand in almost any viewer but since my molecules are rather big I'm looking for a more efficient solution. Regards, Martijn Zwijnenburg ------------------------------------------------------------------------- Martijn Zwijnenburg Lab. of Applied Organic Chemistry and Catalysis Delft University of Technology Julianalaan 136 2628 BL Delft The Netherlands Tel: 0031-(0)152782691 Fax: 0031-(0)152784700 e-mail: M.A.Zwijnenburg@tnw.tudelft.nl web page: http://come.to/tock From chemistry-request@server.ccl.net Mon May 20 09:59:01 2002 Received: from mailhub.cs.uoguelph.ca ([131.104.96.75]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4KDx1130714 for ; Mon, 20 May 2002 09:59:01 -0400 Received: from ccshst01.cs.uoguelph.ca (ccshst01.cs.uoguelph.ca [131.104.96.81]) by mailhub.cs.uoguelph.ca (8.11.6/8.11.6) with ESMTP id g4KDx0l06702; Mon, 20 May 2002 09:59:00 -0400 (EDT) Date: Mon, 20 May 2002 09:58:59 -0400 (EDT) From: Ruth Tanner X-Sender: rtanner@ccshst01.cs.uoguelph.ca To: Martijn Zwijnenburg cc: chemistry@ccl.net Subject: Re: CCL:bond lenghts In-Reply-To: <3CE90DBE.19813.4314342A@localhost> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Perl or Awk could be used to write a script to do such a thing, but I don't know of one presently in existance. Anyone? Ruth On Mon, 20 May 2002, Martijn Zwijnenburg wrote: > Hi, > > I'm looking for a program which can read in the structure of a > molecule (as pdb or xyz) and output a table of bond-lengths (or > atom-atom distances for what it's worth). No difficult analysis > methods needed, just one structure. I'm thinking of an output like: > > Si1-O4 1.644 > Si1-O5 1.643 > etc. etc. > > I can do this by hand in almost any viewer but since my molecules > are rather big I'm looking for a more efficient solution. > > Regards, > > Martijn Zwijnenburg > ------------------------------------------------------------------------- > Martijn Zwijnenburg > Lab. of Applied Organic Chemistry and Catalysis > Delft University of Technology > Julianalaan 136 > 2628 BL Delft > The Netherlands > Tel: 0031-(0)152782691 > Fax: 0031-(0)152784700 > e-mail: M.A.Zwijnenburg@tnw.tudelft.nl > web page: http://come.to/tock > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > -------------------------------------------------------------------- Ruth Tanner rtanner@uoguelph.ca -------------------------------------------------------------------- "Love's way of dealing with us is different from conscience's way. Conscience commands; love inspires. What we do out of love, we do because we want to do it." --- A.J. Toynbee ==================================================================== From chemistry-request@server.ccl.net Mon May 20 10:52:52 2002 Received: from chinon.cnrs-orleans.fr ([163.9.6.107]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4KEqq131722 for ; Mon, 20 May 2002 10:52:52 -0400 Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.11.2/8.11.2) id g4KEots10606; Mon, 20 May 2002 16:50:55 +0200 X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f Sender: hinsen@chinon.cnrs-orleans.fr To: Martijn Zwijnenburg , chemistry@ccl.net Subject: Re: CCL:bond lenghts References: From: Konrad Hinsen Date: 20 May 2002 16:50:55 +0200 In-Reply-To: Message-ID: Lines: 49 User-Agent: Gnus/5.0808 (Gnus v5.8.8) Emacs/20.7 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii On Mon, 20 May 2002, Martijn Zwijnenburg wrote: > Hi, > > I'm looking for a program which can read in the structure of a > molecule (as pdb or xyz) and output a table of bond-lengths (or > atom-atom distances for what it's worth). No difficult analysis > methods needed, just one structure. I'm thinking of an output like: > > Si1-O4 1.644 > Si1-O5 1.643 > etc. etc. > > I can do this by hand in almost any viewer but since my molecules > are rather big I'm looking for a more efficient solution. Here's the program you are looking for: ---------------------------------------------------------------------- > from Scientific.IO.PDB import Structure s = Structure('molecule.pdb') for molecule in s.residues: print print molecule.name pairs = [] for atom1 in molecule.atoms.values(): for atom2 in molecule.atoms.values(): if atom1 != atom2: distance = (atom1.position-atom2.position).length() pairs.append((atom1.name, atom2.name, distance)) pairs.sort(lambda a, b: cmp(a[2], b[2])) for atom1, atom2, distance in pairs: print "%4s - %4s: %f" % (atom1, atom2, distance) ---------------------------------------------------------------------- As a bonus, you get the pairs sorted by increasing distance. Requirements: Python (www.python.org) and ScientificPython (dirac.cnrs-orleans.fr/ScientifciPython/) -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Mon May 20 10:54:00 2002 Received: from simulux.us.es (IDENT:root@[150.214.145.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4KErx131780 for ; Mon, 20 May 2002 10:54:00 -0400 Received: from localhost (rafapa@localhost) by simulux.us.es (8.9.3/8.8.7) with ESMTP id QAA04183 for ; Mon, 20 May 2002 16:55:03 +0200 Date: Mon, 20 May 2002 16:55:03 +0200 (CEST) From: "Rafael R. Pappalardo" To: Subject: CHELP sources. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I am trying to implement the CHELP method in some ab initio code. I have downloaded the sources from http://www.ccl.net/cca/software/SOURCES/FORTRAN/chelpg/new/ directory. Surprisingly the files have lost the fortran format. The lines begin at column 1. Some continuation lines are merged together, etc. The gopher address mentioned does not work anymore. QCPE list the program as not available. Does anybody knows where to get it? It will be wonderfull if it is a version including latest recommendations from Profs. Francl and Chirlian (RCC vol 14). Thanks, -- Dr. Rafael R. Pappalardo Dept. Quimica Fisica, Fac. de Quimica, Univ. de Sevilla. 41012-Sevilla (Spain) e-mail: rafapa@simulux.us.es From chemistry-request@server.ccl.net Mon May 20 11:39:03 2002 Received: from lavoisier.dq.ufscar.br ([200.9.84.145]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4KFd2100863 for ; Mon, 20 May 2002 11:39:03 -0400 Received: from localhost (localhost.dq.ufscar.br [127.0.0.1]) by lavoisier.dq.ufscar.br (Postfix) with ESMTP id 1AB1C223D for ; Mon, 20 May 2002 12:38:58 -0300 (BRT) Received: from dq.ufscar.br (unknown [200.136.225.253]) by lavoisier.dq.ufscar.br (Postfix) with SMTP id CBA1D2234 for ; Mon, 20 May 2002 12:38:56 -0300 (BRT) Date: Mon, 20 May 2002 15:38:56 -0000 To: Subject: ZINDO From: X-Mailer: TWIG 2.7.5 Message-Id: <20020520153856.CBA1D2234@lavoisier.dq.ufscar.br> X-Virus-Scanned: by AMaViS perl-10 Dear CCL'ers, I am very interested in a free source code for the ZINDO program. Known any one if such a copy is available for the public domain? Thanks in advance, Dr. Ademir Camargo From chemistry-request@server.ccl.net Mon May 20 13:15:07 2002 Received: from simulux.us.es (IDENT:root@[150.214.145.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4KHF7104326 for ; Mon, 20 May 2002 13:15:07 -0400 Received: from localhost (rafapa@localhost) by simulux.us.es (8.9.3/8.8.7) with ESMTP id TAA04835; Mon, 20 May 2002 19:16:09 +0200 Date: Mon, 20 May 2002 19:16:08 +0200 (CEST) From: "Rafael R. Pappalardo" To: Jim Kress cc: Subject: Re: CCL:CHELP sources. In-Reply-To: <000701c2001c$6734e800$0201a8c0@hppav> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 20 May 2002, Jim Kress wrote: > Why don't you ask the author? Follow this link: > > http://www.brynmawr.edu/chemistry/mfrancl.html > > Jim > Sorry, I forgot to mention that I sent mails to both of them without success. Rafael > > ----- Original Message ----- > From: "Rafael R. Pappalardo" > To: > Sent: Monday, May 20, 2002 10:55 AM > Subject: CCL:CHELP sources. > > > > Dear all, > > > > I am trying to implement the CHELP method in some ab initio code. > > I have downloaded the sources from > > > > http://www.ccl.net/cca/software/SOURCES/FORTRAN/chelpg/new/ > > > > directory. Surprisingly the files have lost the fortran format. > > The lines begin at column 1. Some continuation lines are merged > > together, etc. > > > > The gopher address mentioned does not work anymore. QCPE list the > > program as not available. > > > > Does anybody knows where to get it? It will be wonderfull if it is a > > version including latest recommendations from Profs. Francl and Chirlian > > (RCC vol 14). > > > > Thanks, > > > > -- > > Dr. Rafael R. Pappalardo > > Dept. Quimica Fisica, Fac. de Quimica, Univ. de Sevilla. 41012-Sevilla > (Spain) > > e-mail: rafapa@simulux.us.es > > > > > > -= This is automatically added to each message by mailing script =- > > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To > Admins > > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net > 70 > > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net > > > > > > > > > > > -- Dr. Rafael R. Pappalardo Dept. Quimica Fisica, Fac. de Quimica, Univ. de Sevilla. 41012-Sevilla (Spain) e-mail: rafapa@simulux.us.es From chemistry-request@server.ccl.net Mon May 20 09:41:35 2002 Received: from mail1-0.chcgil.ameritech.net ([206.141.192.68]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4KDfY130504 for ; Mon, 20 May 2002 09:41:34 -0400 Received: from localhost ([66.73.164.238]) by mail1-0.chcgil.ameritech.net (InterMail vM.4.01.02.17 201-229-119) with ESMTP id <20020520133342.CUHE4339.mail1-0.chcgil.ameritech.net@localhost>; Mon, 20 May 2002 08:33:42 -0500 Date: Mon, 20 May 2002 08:41:24 -0500 Subject: Re: CCL:bond lenghts Content-Type: text/plain; charset=US-ASCII; format=flowed Mime-Version: 1.0 (Apple Message framework v481) Cc: chemistry@ccl.net To: Martijn Zwijnenburg From: Geoff Hutchison In-Reply-To: <3CE90DBE.19813.4314342A@localhost> Message-Id: <470C5643-6BF7-11D6-9B09-0050E4863261@wso.williams.edu> Content-Transfer-Encoding: 7bit X-Mailer: Apple Mail (2.481) On Monday, May 20, 2002, at 07:53 AM, Martijn Zwijnenburg wrote: > I'm looking for a program which can read in the structure of a > molecule (as pdb or xyz) and output a table of bond-lengths (or > atom-atom distances for what it's worth). No difficult analysis > methods needed, just one structure. I'm thinking of an output like: Yes, the original Babel has always been able to do this. It's the "report" file format. (Open Babel can do this too, but it's still in development towards a stable release.) ------- -Geoff Hutchison Ratner/Marks Groups (847) 491-3295 Northwestern Chemistry http://www.chem.nwu.edu/ From chemistry-request@server.ccl.net Mon May 20 14:00:58 2002 Received: from mx.seanet.com ([199.181.164.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4KI0w106005 for ; Mon, 20 May 2002 14:00:58 -0400 Received: from Debug (ssl.seanet.com [199.181.164.13]) by mx.seanet.com (8.11.6/8.11.6) with SMTP id g4KI0eY03377; Mon, 20 May 2002 11:00:40 -0700 (PDT) Message-Id: <200205201800.g4KI0eY03377@mx.seanet.com> To: , From: Mark Thompson Subject: Re: CCL:ZINDO Date: Mon, 20 May 2002 11:00:44 US/Pacific X-Mailer: Endymion MailMan Professional Edition v3.0.35 Dear Ademir, The original ZINDO program from the Zerner group is now commercially distributed by Accelrys. To my knowledge the source is not publicly available, nor am I certain how well Accelrys is maintaining the code (it was very difficult to maintain and enhance). Other sources of ZINDO capability are (in alphabetical order): 1. ArgusLab (http://www.arguslab.com) 2. CAChe 3. Gaussian 4. HyperChem All of the above are commercial programs and not available in source form as far as I know. Cheers, Mark > Dear CCL'ers, > > I am very interested in a free source code for the ZINDO program. Known > any one if such a copy is available for the public domain? > > Thanks in advance, > > Dr. Ademir Camargo > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > ======================================= Mark Thompson, Ph.D. Planaria Software Seattle, WA http://www.arguslab.com ======================================= From chemistry-request@server.ccl.net Mon May 20 07:51:50 2002 Received: from web12805.mail.yahoo.com ([216.136.174.40]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g4KBpn128846 for ; Mon, 20 May 2002 07:51:50 -0400 Message-ID: <20020520115146.8127.qmail@web12805.mail.yahoo.com> Received: from [64.94.101.217] by web12805.mail.yahoo.com via HTTP; Mon, 20 May 2002 04:51:46 PDT Date: Mon, 20 May 2002 04:51:46 -0700 (PDT) From: amor san juan Subject: benA.pdbq file example distribution:Autodock3 To: chemistry@ccl.net Cc: sanner@scripps.edu MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear AutoDockers: Is the benA.mol2 a Sybyl mol2 file format generated? I can't start my docking experiment to my samples due to mismatched data generated from benA.pdbq (file example distribution) as compared to my generated ben.pdbq. The procedure I did is: ben --------> ben.mol ------->ben.mol------> ben.pdbq chemsketch babel ADT To my understanding, commercially Insight or Sybyl had been used in preparing the ligands. Would someone clarify this to me? The problem I encountered is data coordinates produced > from chemsketch does not match from file example distribution. Is it logical for me to induced myself to find an alternative freeware (besides chemsketch) to draw the ligand. I tried converting the 2D ben.mol structure to 3D however, there is no file converter > from 's3d' to 'mol' file. Thanks in advance for time given. Sincerely, Amor San Juan University of the Philippines-Diliman __________________________________________________ Do You Yahoo!? LAUNCH - Your Yahoo! Music Experience http://launch.yahoo.com From chemistry-request@server.ccl.net Mon May 20 10:25:45 2002 Received: from nikias.cc.uoa.gr ([195.134.68.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4KEPi131110 for ; Mon, 20 May 2002 10:25:44 -0400 Received: from localhost (jkerkin@localhost) by nikias.cc.uoa.gr (8.9.3/8.9.3) with SMTP id RAA09613; Mon, 20 May 2002 17:25:40 +0300 (EET DST) Date: Mon, 20 May 2002 17:25:40 +0300 (EET DST) From: Ioannis Kerkines To: Martijn Zwijnenburg cc: chemistry@ccl.net Subject: Re: CCL:bond lenghts In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I think this can be easily done with the (commercial) program Chem3D (part of the Chemoffice suite). After importing the initial structure, you can view the coordinates in many ways, one of which is a table of internal coordinates which should be enough to specify the full structure of your molecule. You can then e.g. copy + paste this table to other applications like Word or Excel and apply any desired modifications. Best Ioannis On Mon, 20 May 2002, Ruth Tanner wrote: > > Perl or Awk could be used to write a script to do such a thing, > but I don't know of one presently in existance. Anyone? > > Ruth > > On Mon, 20 May 2002, Martijn Zwijnenburg wrote: > > > Hi, > > > > I'm looking for a program which can read in the structure of a > > molecule (as pdb or xyz) and output a table of bond-lengths (or > > atom-atom distances for what it's worth). No difficult analysis > > methods needed, just one structure. I'm thinking of an output like: > > > > Si1-O4 1.644 > > Si1-O5 1.643 > > etc. etc. > > > > I can do this by hand in almost any viewer but since my molecules > > are rather big I'm looking for a more efficient solution. > > > > Regards, > > > > Martijn Zwijnenburg > > ------------------------------------------------------------------------- > > Martijn Zwijnenburg > > Lab. of Applied Organic Chemistry and Catalysis > > Delft University of Technology > > Julianalaan 136 > > 2628 BL Delft > > The Netherlands > > Tel: 0031-(0)152782691 > > Fax: 0031-(0)152784700 > > e-mail: M.A.Zwijnenburg@tnw.tudelft.nl > > web page: http://come.to/tock > > > > > > > > > > > > > > -------------------------------------------------------------------- > Ruth Tanner rtanner@uoguelph.ca > -------------------------------------------------------------------- > "Love's way of dealing with us is different from conscience's way. > Conscience commands; love inspires. What we do out of love, we do > because we want to do it." --- A.J. Toynbee > ==================================================================== > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Mon May 20 14:21:02 2002 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4KIL2106942 for ; Mon, 20 May 2002 14:21:02 -0400 Received: from arlen.ccl.net (arlen.ccl.net [192.148.249.10]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.0) with ESMTP id g4KIL3101341; Mon, 20 May 2002 14:21:03 -0400 (EDT) Date: Mon, 20 May 2002 14:21:02 -0400 (EDT) From: Jan Labanowski To: chemistry@ccl.net, mel@asdn.net cc: Jan Labanowski Subject: Moscow (Nano & Giga) & Cracow (E-MRS) Meetings: Final Call for Papers Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Colleague, This is the final call to contribute a paper to very interesting Conferences in mid September of 2002: Nano & Giga Challenges in Microelectronics, Sep 10-13, Moscow, -------------------------------------------------------------- and Software Development for Process & Materials Design, Sept 15-19, Cracow. ------------------------------------------------------------------------ The deadline for abstract submission is until the end of this month, so please do not procrastinate. ========================================================================= | Nano & Giga Challenges in Microelectronics, Sep 10-13, 2002. Moscow | ========================================================================= http://asdn.net/moscow This conference brings together highest caliber specialists from all over the world, THEORETICIANS and EXPERIMENTALISTS alike, to answer the the question: What next? The wide range of problems (atomic scale design, magnetic materials, optoelectronics, FETs, nanotubes, clusters, nonoscale reliability, etc.) is discussed on the highest level. Yet, the second part of the conference is a Summer School with the world experts providing introduction to their specialties. A great opportunity to learn more in your specific field and to venture into adjacent areas. We hope that bringing this mix of leaders in this field will results in new ideas, a few converts, and plenty to write about in your grant proposals for years to come. Visit the Conference site: http://asdn.net/moscow Even if you cannot come, it will be the time well spend and you will learn about hot issues being discussed at the conference. =========================================================================== | Software Development for Process & Materials Design, Sept 15-19, Cracow | =========================================================================== http://asdn.net/emrs/fall2002 The focus of this symposium is: software development and methodology. Again it can be of interest not only to computationally oriented materials scientists and engineers, but also for those experimentalists who want to incorporate powerful and promising computational methods in their research. The following topics will be discussed: Quantum Monte Carlo, ab initio and (semi)empirical approaches, multiscale, molecular modeling, combinatorial, HTS, QSAR/QSPR, biotech, approaches to process design, and cheminformatics. The representative examples of applications will also be available. The symposium has an educational component and keynote speakers will provide necessary background to follow the more advanced talks. It is a rare opportunity for experimentalists to learn about available software and approaches from the experts. The beauty of Cracow, and the importance of this emerging research basin of Central Europe should help those undecided. Please visit the symposium pages at: http://asdn.net/emrs/fall2002 and peek at additional symposia and plenary sessions of this E-MRS Fall 2002 meeting by following links at the Web site. ====================================================================== If you have more time, you may want to conveniently score two meetings (as will do the organizers). If you have additional questions contact the organizers on the web site, or send e-mail to the undersigned. Thank you for your patience, and accept our warmest invitation: Jan Labanowski, Ph.D., Senior Scientist Ohio Supercomputer Cnter Columbus, Ohio 43212-1163, USA E-mail: jkl@asdn.net For the organizing committee: Jim Greer (National Microelectronics Research Centre, Cork, Ireland) Anatoli A. Korkin (Motorola Inc., Mesa, AZ, USA) Stanislaw A. Kucharski (University of Silesia, Katowice, Poland). From chemistry-request@server.ccl.net Mon May 20 17:46:53 2002 Received: from sas.asc.hpc.mil ([129.48.244.126]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4KLkq116341 for ; Mon, 20 May 2002 17:46:52 -0400 Received: from asc.hpc.mil (wk32.asc.hpc.mil [129.48.245.32]) by sas.asc.hpc.mil (8.11.6/8.11.6) with ESMTP id g4KLknI704406 for ; Mon, 20 May 2002 17:46:49 -0400 (EDT) Sender: duanx@asc.hpc.mil Message-ID: <3CE96EC9.5716300@asc.hpc.mil> Date: Mon, 20 May 2002 17:46:49 -0400 From: XIAOFENG FRANK DUAN Organization: CSC X-Mailer: Mozilla 4.79 [en] (X11; U; IRIX 6.5 IP22) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: ROMP2 gradients Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all, I was wondering if there are any programs that can do ROMP2 gradients? Thanks! Frank