From chemistry-request@server.ccl.net Tue Apr 9 23:49:04 2002 Received: from web12805.mail.yahoo.com ([216.136.174.40]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g3A3n3p22883 for ; Tue, 9 Apr 2002 23:49:04 -0400 Message-ID: <20020410034857.5671.qmail@web12805.mail.yahoo.com> Received: from [203.87.132.164] by web12805.mail.yahoo.com via HTTP; Tue, 09 Apr 2002 20:48:57 PDT Date: Tue, 9 Apr 2002 20:48:57 -0700 (PDT) From: amor san juan Subject: Mkgpf3 & Mkdpf3 executables:AutoDock3 To: Ruth Huey Cc: chemistry@ccl.net In-Reply-To: <3CB1E6E7.DBCF00E0@scripps.edu> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Sir: Im working on AutoDock3 at linux. The awk programs consisting of mkgpf3,mkdpf3,deftors & many more are located in share bin. I like to ask your diagnosis on the following series of commands I input: 1) I execute mkgpf3 ..................................... [dostaas@csrc share]$ ./mkgpf3 ________________________________________________________________________________ mkgpf3 Version 3.0.4 (C) 1999, Garrett Morris, TSRI. Ligand = "", Macromolecule = "". Making ".gpf", based on the atom types found in "" gpf3gen: Command not found. pdbcen: Command not found. csplit: `/gridcenter/': match not found cat: xx02: No such file or directory Completed making grid parameter file: ".gpf" _______________________________________________________ The mkgpf3 is looking for gpf3gen & pdbcen.Then, 2)I searched for them: [dostaas@csrc share]$ ./gpf3gen gawk: fatal: can't open source file "/gpf3gen.awk" for reading (No such file or directory) [dostaas@csrc share]$ ./pdbcen _______________________________________________________ It calls for gpf3gen.awk. Next, i look for it: [dostaas@csrc dist305]$ cd share [dostaas@csrc share]$ ./gpf3gen.awk ./gpf3gen.awk: BEGIN: command not found ./gpf3gen.awk: ON: command not found ./gpf3gen.awk: OFF: command not found ./gpf3gen.awk: PROTEIN_ATOMTYPES: command not found ./gpf3gen.awk: ALL_TYPES: command not found ./gpf3gen.awk: line 9: syntax error near unexpected token `length(A' ./gpf3gen.awk: line 9: ` NUM_TYPES = length(ALL_TYPES)' [dostaas@csrc share]$ ********************************** The bottom line is it cant find the awk programs specified. With the abovementioned commands & reply, I think some files are CORRUPTED at the share bin. What i did was to untar again the tar.gz file but, just the same thing happens. Needing your suggestions. Amor San Juan University of the Philippines-Diliman __________________________________________________ Do You Yahoo!? Yahoo! Tax Center - online filing with TurboTax http://taxes.yahoo.com/ From chemistry-request@server.ccl.net Wed Apr 10 04:02:38 2002 Received: from as1200.organik.uni-erlangen.de ([131.188.128.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3A82bp28015 for ; Wed, 10 Apr 2002 04:02:37 -0400 Received: from chemie.uni-erlangen.de (equinox.chemie.uni-erlangen.de [131.188.128.90]) by as1200.organik.uni-erlangen.de (8.8.7/8.1.11-FAU) with ESMTP id KAA21817 for ; Wed, 10 Apr 2002 10:02:31 +0200 (MET DST) Sender: Harald.Lanig@Organik.Uni-Erlangen.DE Message-ID: <3CB3F1EC.63F8A973@chemie.uni-erlangen.de> Date: Wed, 10 Apr 2002 10:03:56 +0200 From: Harald Lanig Organization: Computer-Chemie-Centrum X-Mailer: Mozilla 4.77 [de] (X11; U; Linux 2.4.4-4GB i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: 16th Molecular Modelling Workshop - May 07-08, 2002 in Darmstadt, Germany Content-Type: multipart/alternative; boundary="------------69C182066A64E811041D7712" --------------69C182066A64E811041D7712 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear list members, let me please point your attention to 16th Molecular Modelling Workshop taking place in Darmstadt, Germany from May 07 to 08, 2002. The registration deadline is now April 16, 2002. We are happy to announce two Keynote lectures: Ursula Röthlisberger, ETH Zürich and Jürgen Brickmann, TU Darmstadt The Second Circular it out now and available following the URL http://www.pc.chemie.tu-darmstadt.de/mmws/2002/circ2.shtml There are still a few Poster and Speaker slots free! Although the official conference language is German, this information may be useful to a lot of readers of this list. For further information please see the URL http://www.pc.chemie.tu-darmstadt.de/mmws/ Kind regards, Harald Lanig -- ------------------------------------------------------------------------ Dr. Harald Lanig Universitaet Erlangen/Nuernberg Computer-Chemie-Centrum Naegelsbachstr. 25, D-91052 Erlangen oder Lehrstuhl fuer Schuhstrasse 19 Pharmazeutische Chemie D-91052 Erlangen, Germany Phone +49(0)9131-85 26525 Mailto:lanig@chemie.uni-erlangen.de Fax +49(0)9131-85 26565 http://www.ccc.uni-erlangen.de/lanig ------------------------------------------------------------------------ --------------69C182066A64E811041D7712 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear list members,

let me please point your attention to 16th Molecular Modelling Workshop taking place in Darmstadt, Germany from May 07 to 08, 2002. The  registration deadline is now April 16, 2002.

We are happy to announce two Keynote lectures:

Ursula Röthlisberger, ETH Zürich and Jürgen Brickmann, TU Darmstadt

The Second Circular it out now and available following the URL http://www.pc.chemie.tu-darmstadt.de/mmws/2002/circ2.shtml

There are still a few Poster and Speaker slots free!

Although the official conference language is German, this information may be useful to a lot of readers of this list. For further information please see the URL

http://www.pc.chemie.tu-darmstadt.de/mmws/
 

Kind regards,
Harald Lanig 

-- 
------------------------------------------------------------------------
 Dr. Harald Lanig            Universitaet Erlangen/Nuernberg
 Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen
 oder
 Lehrstuhl fuer              Schuhstrasse 19
 Pharmazeutische Chemie      D-91052 Erlangen, Germany
 
 Phone +49(0)9131-85 26525   Mailto:lanig@chemie.uni-erlangen.de
 Fax   +49(0)9131-85 26565   http://www.ccc.uni-erlangen.de/lanig
------------------------------------------------------------------------
 

 
 
 
  --------------69C182066A64E811041D7712-- From chemistry-request@server.ccl.net Wed Apr 10 04:05:18 2002 Received: from jivdhan.unipune.ernet.in ([196.1.114.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3A85Cp28088 for ; Wed, 10 Apr 2002 04:05:17 -0400 Received: from chem.unipune.ernet.in (chem.unipune.ernet.in [196.1.114.10]) by jivdhan.unipune.ernet.in (8.11.6/8.11.6) with ESMTP id g3A8BiZ07975; Wed, 10 Apr 2002 13:41:44 +0530 Received: (from gadre@localhost) by chem.unipune.ernet.in (8.9.3/8.8.7) id NAA06158; Wed, 10 Apr 2002 13:31:49 +0530 Date: Wed, 10 Apr 2002 13:31:49 +0530 From: gadre@chem.unipune.ernet.in Message-Id: <200204100801.NAA06158@chem.unipune.ernet.in> To: CHEMISTRY@server.ccl.net Subject: Some help locating publications.. Cc: gadre@chem.unipune.ernet.in Dear Sirs and Madams : A few years' ago, we published in Portugalea Fisica two extended abstarcts (special issue which published the proceedings of SAGANORE IX conference). Unfortunately I do not have the papers and also the journal is not available in India very easily. The papres were short (2/3 printed pages) and were published in 1988. Could someone (prbably from Portugal/Spain/France) help? Thanks a lot!..........Shridhar GAdre From chemistry-request@server.ccl.net Wed Apr 10 14:36:36 2002 Received: from jilau1.Colorado.EDU ([128.138.140.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3AIaap12724 for ; Wed, 10 Apr 2002 14:36:36 -0400 Received: from ixion.colorado.edu (ixion.Colorado.EDU [128.138.107.182]) by jilau1.Colorado.EDU (8.11.6/8.11.6/UnixOps+Hesiod) with ESMTP id g3AIaVM61990 for ; Wed, 10 Apr 2002 12:36:31 -0600 (MDT) Subject: G98: Massage and %Chk From: The Matt To: chemistry@ccl.net Content-Type: multipart/signed; micalg=pgp-sha1; protocol="application/pgp-signature"; boundary="=-zY1G6x9GfaGmQVZyJCde" X-Mailer: Ximian Evolution 1.0.3 (1.0.3-1) Date: 10 Apr 2002 12:36:31 -0600 Message-Id: <1018463791.17541.23.camel@ixion.colorado.edu> Mime-Version: 1.0 --=-zY1G6x9GfaGmQVZyJCde Content-Type: text/plain Content-Transfer-Encoding: quoted-printable I feel kind of dumb for asking this, but I can't seem to get Gaussian to do what I want, and it's probably pretty simple. Namely, I am trying to do some BSSE jobs all in the same input file. (I have access to Rev. A.7, so I can't use the Counterpoise keyword.)=20 Naively, I try this: %Chk=3Dtrial.chk # B3LYP/STO-3G SCF=3D(QC,Tight) Opt=3DModRedun NoSymm ...molecule spec, doing Cl-...CO2, this job for opt.... --Link1-- %Chk=3Dtrial.chk # B3LYP/STO-3G SCF=3D(QC,Tight) Massage Geom=3DCheck ...Cl- nucleus zeroed, use optimized geom from above... 1 Nuc 0.0 --Link1-- %Chk=3Dtrial.chk # B3LYP/STO-3G SCF=3D(QC,Tight) Massage Geom=3DCheck ...Zero out CO2, want to use OPT geom from two steps ago... 2 Nuc 0.0 3 Nuc 0.0 4 Nuc 0.0 So, the first two steps work great. But the third explodes since in reading the checkfile, it also reads that the Cl nucleus is Massage-d to zero. So, the second Massage rubs out all the nuclei, and hilarity ensues (hilarity=3Dsegmentation faults, crashes, &c.)! How can I get it so that Gaussian reads the original optimized structure in both BSSE steps, without it transferring the first Massage to the third step? (Essentially, make trial.chk read-only after the first step.) Or will I be doing this in three jobs instead? Thanks, Matt Thompson --=20 "And isn't sanity really just a one-trick pony, anyway? I mean, all you get is one trick, rational thinking, but when you're good and crazy, ooh ooh ooh, the sky's the limit!" -- The Tick TheMatt -- http://ucsub.colorado.edu/~thompsma/Home.html --=-zY1G6x9GfaGmQVZyJCde Content-Type: application/pgp-signature; name=signature.asc Content-Description: This is a digitally signed message part -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.6 (GNU/Linux) Comment: For info see http://www.gnupg.org iD8DBQA8tIYu0XRaGMGO968RAsa9AJ9lY3h0XICn8xoKawX8zlE1tHNb5QCgrq0f n0h4rY2gXquoCGkQ7IZqZmo= =qP7K -----END PGP SIGNATURE----- --=-zY1G6x9GfaGmQVZyJCde-- From chemistry-request@server.ccl.net Wed Apr 10 16:15:08 2002 Received: from sd.accelrys.com ([146.202.0.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3AKF8p15509 for ; Wed, 10 Apr 2002 16:15:08 -0400 Received: (from osman@localhost) by sd.accelrys.com (8.11.0/8.11.0) id g3AKEll21959 for chemistry@server.ccl.net; Wed, 10 Apr 2002 13:14:47 -0700 Received: from OGUNER-LAP.accelrys.com (dp-dhcp29.sd.accelrys.com [172.30.199.29] (may be forged)) by sd.accelrys.com (8.11.0/8.11.0) with ESMTP id g3AKEjV21914; Wed, 10 Apr 2002 13:14:45 -0700 Message-Id: <5.1.0.14.2.20020410130621.02a160e8@sparky2.sd.accelrys.com> X-Sender: osman@sparky2.sd.accelrys.com X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Wed, 10 Apr 2002 13:14:11 -0700 To: chemistry@server.ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, qsar_society@accelrys.com From: "Osman F. Guner" Subject: Second Call for papers - virtual High-Throughput Screening Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_9331598==_.ALT" --=====================_9331598==_.ALT Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: quoted-printable We are approaching the deadline (April 19th) for submitting papers for this= =20 symposium. Current contributions are in the areas of fast docking-scoring,= =20 distributed systems, and pharmacophore or property-based database=20 screening. We will likely have several half-day sessions focusing the=20 papers on the above topics. Please submit your abstracts on a timely fashion. If you have any=20 questions on the appropriateness of your work to this symposium, feel free= =20 to contact me. Cheers...Osman VIRTUAL HIGH-THROUGHPUT SCREENING At Fall ACS meeting in Boston (August 18-22, 2002) Sponsored by the Chemical Information Division (CINF) Co-sponsored by Division of Medicinal Chemistry (MEDI), and Division of Computers in Chemistry (COMP) As the combinatorial chemistry and high-throughput screening technologies=20 settle down more or less as established technologies, the need for=20 managing, analyzing, and mining very large amounts of data that is=20 generated through these technologies is still an active problem. Virtual=20 high-throughput screening is one of the solutions that has been evolving:=20 ability to screen large compound libraries or databases for active hits or= =20 leads. We would like to invite you to contribute to this symposium. Topics= =20 to be covered include informatics challenges, high-throughput docking and=20 scoring, property-based screening, and others. Please use the OASys to submit your abstract. You can access the CINF=20 symposia at OASys via http://oasys.acs.org/oasys.htm. The deadline for=20 submitting abstracts is April 19th. --- Osman F. G=FCner, Ph.D. Sr. Director, Lead Identification & Optimization Accelrys Inc. (858) 799-5341 osman@accelrys.com http://www.accelrys.com --=====================_9331598==_.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable We are approaching the deadline (April 19th) for submitting papers for this symposium.  Current contributions are in the areas of fast docking-scoring, distributed systems, and pharmacophore or property-based database screening.  We will likely have several half-day sessions focusing the papers on the above topics. 

Please submit your abstracts on a timely fashion.  If you have any questions on the appropriateness of your work to this symposium, feel free to contact me.

Cheers...Osman

VIRTUAL HIGH-THROUGHPUT SCREENING

At Fall ACS meeting in Boston (August 18-22, 2002)

Sponsored by the Chemical Information Division (CINF)
Co-sponsored by Division of Medicinal Chemistry (MEDI),
and Division of Computers in Chemistry (COMP)

As the combinatorial chemistry and high-throughput screening technologies settle down more or less as established technologies, the need for managing, analyzing, and mining very large amounts of data that is generated through these technologies is still an active problem. Virtual high-throughput screening is one of the solutions that has been evolving: ability to screen large compound libraries or databases for active hits or leads. We would like to invite you to contribute to this symposium. Topics to be covered include informatics challenges, high-throughput docking and scoring, property-based screening, and others.

Please use the OASys to submit your abstract. You can access the CINF symposia at OASys via http://oasys.acs.org/oasys.htm. The deadline for submitting abstracts is April 19th.

---
Osman F. G=FCner, Ph.D.
Sr. Director,  Lead Identification & Optimization
Accelrys Inc.   (858) 799-5341
osman@accelrys.com        http://www.accelrys.= com --=====================_9331598==_.ALT-- From chemistry-request@server.ccl.net Wed Apr 10 13:31:12 2002 Received: from sarraute.uol.com.br ([200.231.206.182]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3AHV4p10613 for ; Wed, 10 Apr 2002 13:31:12 -0400 Received: from walters.uol.com.br ([200.231.206.195]) by sarraute.uol.com.br (8.9.1/8.9.1) with ESMTP id OAA17677 for ; Wed, 10 Apr 2002 14:33:06 -0300 (BRT) Received: (from nobody@localhost) by walters.uol.com.br (8.9.1/8.9.1) id OAA13858; Wed, 10 Apr 2002 14:30:29 -0300 (BRT) Date: Wed, 10 Apr 2002 14:30:29 -0300 (BRT) From: alex.msilva@uol.com.br Message-Id: <200204101730.OAA13858@walters.uol.com.br> Content-Type: text/plain Content-Disposition: inline Mime-Version: 1.0 X-Mailer: MIME-tools 4.104 (Entity 4.117) To: chemistry@ccl.net X-Originating-Ip: [146.164.1.24] Subject: CCSD(T) Reply-To: alex.msilva@uol.com.br Hi, I´m trying to calculate a system at level CCSD(T) using Gaussian, and I get the following erro mesage in the .log file: #N CCSD(T) FREQ GEN GFPRINT UNIT=AU .... .... ----------------- Symbolic Z-matrix: Charge = 1 Multiplicity = 1 ... geometry input.. ... followed by NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF-NEF- NUMERICAL EIGENVECTOR FOLLOWING MINIMUM SEARCH INITIALIZATION PASS ************************************************ ** ERROR IN INITNF. NUMBER OF VARIABLES ( 0) ** ** INCORRECT (SHOULD BE BETWEEN 1 AND 50) ** ************************************************ Error termination via Lnk1e in /mnt/bach/ibm/g98/bsd/l114.exe. What happened? Can somebody help me? Thanks in advance, Alexander. From chemistry-request@server.ccl.net Wed Apr 10 17:49:27 2002 Received: from sun1.udg.es ([130.206.45.89]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3ALnQp18417 for ; Wed, 10 Apr 2002 17:49:27 -0400 Received: from iqc.udg.es (woodstock.udg.es [130.206.128.118]) by sun1.udg.es (8.9.3/8.9.3/otb) with ESMTP id XAA22369; Wed, 10 Apr 2002 23:48:14 +0100 (WET DST) Message-ID: <3CB4D01F.60000@iqc.udg.es> Date: Thu, 11 Apr 2002 01:51:59 +0200 From: Pedro Salvador Sedano User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4.1) Gecko/20020314 Netscape6/6.2.2 X-Accept-Language: en-us MIME-Version: 1.0 To: The Matt CC: chemistry@ccl.net Subject: Re: CCL:G98: Massage and %Chk References: <1018463791.17541.23.camel@ixion.colorado.edu> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear MAtt I think the best solution will probably be to MASSAGE the Cl atom in the last calculation too..back to it's original charge 1 nuc 17.0 Pedro -- -------------------------------------------------------------------- Pedro Salvador Sedano Ph.D. Student I'll stare the sundown, Institut de Quimica Computacional untill my eyes go blind. Universitat de Girona I won't change direction, Campus Montilivi 17071, Girona,Spain and I won't change my mind. iqc.udg.es/~perico -------------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Apr 10 19:49:48 2002 Received: from mxout3.cac.washington.edu ([140.142.32.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3ANnmp21237 for ; Wed, 10 Apr 2002 19:49:48 -0400 Received: from mailscan-out1.cac.washington.edu (mailscan-out1.cac.washington.edu [140.142.32.17]) by mxout3.cac.washington.edu (8.12.1+UW01.12/8.12.1+UW02.01) with SMTP id g3ANng8J010684 for ; Wed, 10 Apr 2002 16:49:42 -0700 Received: FROM dante30.u.washington.edu BY mailscan-out1.cac.washington.edu ; Wed Apr 10 16:49:41 2002 -0700 Received: from localhost (jzheng73@localhost) by dante30.u.washington.edu (8.12.1+UW01.12/8.12.1+UW02.01) with ESMTP id g3ANnfBw102842 for ; Wed, 10 Apr 2002 16:49:41 -0700 Date: Wed, 10 Apr 2002 16:49:41 -0700 (PDT) From: "J. Zheng" To: chemistry@ccl.net Subject: reduced protein models In-Reply-To: <3CB4D01F.60000@iqc.udg.es> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLer: I have a general question about the protein simulation. For protein simulation, force field is important issue. As I know as far, most of persons use different force fields such as Charmm, Gromas, Amber etc to describe different protein systems with all-atoms model. Sometimes protein is so huge that we have to consider another way to deal with it. For example, we introduce new algorithm (Cell multipole method, PPPM) to reduce computation time, or we resort to parallel program. I am curious that does anyone has develop the general force field (epslo, sigma, charge) for only 20 acid amio residues if we treat each residue as one atom. If yes, could you please give me a reference paper? Now I am working on one protein simulation. I was just thinking about which way I should go. I will appreciate for any suggestion. good day. jie ----------------------------------------------- | JIE ZHENG | | Department of Chemical Engineering | | University of Washington | | Seattle, WA 98105, USA | ----------------------------------------------- | Tel: (206) 616-6510 (o) | | Email: jzheng73@u.washington.edu | | Webpg: students.washington.edu/jzheng73 | -----------------------------------------------