From chemistry-request@server.ccl.net Tue Nov 9 02:48:16 1999 Received: from md2.huji.ac.il (md2.huji.ac.il [132.64.169.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA14546 for ; Tue, 9 Nov 1999 02:48:13 -0500 Received: from md2.huji.ac.il (amimac2.md.huji.ac.il [132.64.165.60]) by md2.huji.ac.il (8.9.3/8.9.3) with ESMTP id JAA04872 for ; Tue, 9 Nov 1999 09:43:41 +0200 (IST) Message-ID: <3827CFCD.71D2E148@md2.huji.ac.il> Date: Tue, 09 Nov 1999 10:39:57 +0300 From: tzvika aviv Reply-To: tzvika_a@md2.huji.ac.il X-Mailer: Mozilla 4.03 (Macintosh; I; PPC) MIME-Version: 1.0 To: chemistry@ccl.net Subject: autodock and nawk Content-Type: text/plain; charset=us-ascii; x-mac-type="54455854"; x-mac-creator="4D4F5353" Content-Transfer-Encoding: 7bit I am a new user of autodock3. when running "gpf3gen" script on the example file "xk2a.pdbq" I get the error massage: "gpf3gen[19]: usr/bin/nawk: arg list too long. " I am using sgi Octane machine (IRIX64). Do you know what can I do about it? thanks Tzvika Aviv e-mail: tzvika_a@md.huji.ac.il at the Pharmacy School Hebrew University Jerusalem From chemistry-request@server.ccl.net Tue Nov 9 07:25:25 1999 Received: from falcon.kvac.uu.se (falcon.kvac.uu.se [130.238.70.84]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA16634 for ; Tue, 9 Nov 1999 07:25:24 -0500 Received: from wolf.kvac.uu.se (wolf.kvac.uu.se [130.238.70.83]) by falcon.kvac.uu.se (8.8.6/8.8.6) with SMTP id NAA17569 for <@falcon.kvac.uu.se:CHEMISTRY@ccl.net>; Tue, 9 Nov 1999 13:17:56 +0100 (CET) Received: by wolf.kvac.uu.se (950413.SGI.8.6.12/930416.SGI) for CHEMISTRY@ccl.net id NAA16657; Tue, 9 Nov 1999 13:17:55 +0100 From: "Yanni Wang" Message-Id: <9911091317.ZM16655@wolf.kvac.uu.se> Date: Tue, 9 Nov 1999 13:17:55 +0000 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@ccl.net Subject: Goin Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii -- ******************************************************************** Yanni Wang | Phone: +46 18 471 6840 Department of Quantum Chemistry | Fax: +46 18 50 24 02 Uppsala University | E-mail: wangyn@kvac.uu.se Box 518 S-751 20 Uppsala, Sweden From chemistry-request@server.ccl.net Mon Nov 8 16:59:40 1999 Received: from mail-d.bcc.ac.uk (mail-d.bcc.ac.uk [144.82.100.24]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA12310 for ; Mon, 8 Nov 1999 16:59:39 -0500 Received: from dns (actually host oganov-jpb98.geol.ucl.ac.uk) by mail-d.bcc.ac.uk with SMTP (XT-PP); Mon, 8 Nov 1999 21:52:36 +0000 Message-ID: <003601bf2a34$60b1e340$072c2880@ucl.ac.uk> Reply-To: "Artem R. Oganov" From: "Artem R. Oganov" To: chemistry Subject: CCL: summary on MD-trajectories animations Date: Mon, 8 Nov 1999 21:58:23 -0000 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0033_01BF2A34.606EBFC0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 This is a multi-part message in MIME format. ------=_NextPart_000_0033_01BF2A34.606EBFC0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCL'ers, =20 My original enquiery was : I am looking for a program to animate MD trajectories, with polyhedral representation of crystal structures. I shall be grateful for any suggections, and summarise them. Also, does anyone know what is the = Web-site of Babel? Many thanks to Keith Refson, Robert Best and Ricardo Grau Crespo, whose = replies (slightly shortened) I summarise below: Keith Refson : Cerius 2 does this I think. But perhaps you are looking for something free. You probably need the MD modules as well as the crystal builder. AVS : there's Larry Finger's "crystal" AVS module which can be used for polyhedral representations. And you can use AVS to animate. However it has it's own unique structure format files. On a Win32 PC there's MSI's free WebLab viewer which I believe will do=20 this. I'm not aware of anything free for unix which does. Babel is pretty useless at converting between periodic crystal structure files and usually loses all symmetry and unit cell information. I have written some perl scripts for converting between PDB/Schakal and CASTEP formats if you are interested. They are in ftp://ftp.earth.ox.ac.uk/pub/keith/cteptouts.tar.gz Robert Best : =20 A good program for displaying trajectories and doing analysis is = gopenmol, available from http://laaksonen.csc.fi/gopenmol. Although the emphasis=20 is on analysis of amorphous systems, there is a facility for drawing = cubic cells, and you can draw any kind of cell using the built-in tcl = scripting. Of course there are crystallographic programs which make the cell = drawing easier, but I don't know of any that have the ability to display=20 trajectories as well. Ricardo Grau Crespo : Babel lives in a lot of places on the net, but the "official" distribution site is http://www.eyesopen.com/babel.html ********************************************************************** Artem R. Oganov, = =20 Doctorate Student in Crystallography and Mineral Physics,=20 Dept. of Geological Sciences, = =20 University College London, = =20 Gower Street, = =20 London WC1E 6BT, = =20 U.K. = =20 E-mail : a.oganov@ucl.ac.uk = Tel. : +44 (0)171-419-3449 Fax : +44 (0)171-387-1612 = =20 ********************************************************************** ------=_NextPart_000_0033_01BF2A34.606EBFC0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear=20 CCL'ers,
 
My original enquiery was :
I am = looking for a program=20 to animate MD trajectories, with polyhedral
representation of crystal = structures. I shall be grateful for any
suggections, and summarise=20 them. Also, does anyone know what is the Web-site
of = Babel?
Many=20 thanks to Keith Refson, Robert Best and Ricardo Grau Crespo, whose = replies=20 (slightly shortened) I summarise below:
 
Keith Refson :
Cerius 2 does this I think.  But = perhaps you=20 are looking for something
free.  You probably need the MD = modules as=20 well as the crystal builder.
AVS : there's Larry Finger's = "crystal" AVS=20 module which can be used for
polyhedral representations.  And = you can=20 use AVS to animate.  However
it has it's own unique structure = format=20 files.

On a Win32 PC there's MSI's free WebLab viewer which I = believe=20 will do
this.  I'm not aware of anything free for unix which=20 does.

Babel is pretty useless at converting between periodic=20 crystal
structure files and usually loses all symmetry and unit=20 cell
information.  I have written some perl scripts for = converting=20 between
PDB/Schakal and CASTEP formats if you are interested.
They = are in=20 ftp://ftp.ea= rth.ox.ac.uk/pub/keith/cteptouts.tar.gz

Robert Best : 
A good program for displaying = trajectories and=20 doing analysis is gopenmol,
available from http://laaksonen.csc.fi/gopenmo= l.=20 Although the emphasis
is on analysis of amorphous systems, there is = a=20 facility for drawing cubic
cells, and you can draw any kind of cell = using the=20 built-in tcl scripting.
Of course there are crystallographic programs = which=20 make the cell drawing
easier, but I don't know of any that have the = ability=20 to display
trajectories as well.
 
 
Ricardo Grau Crespo :
Babel lives in a lot of places on the = net,
but=20 the "official" distribution site is
http://www.eyesopen.com/babel= .html
 
 
****************************************************************= ******
Artem=20 R.=20 Oganov,           =             &= nbsp;           &n= bsp;           &nb= sp;           &nbs= p;    =20
Doctorate Student in Crystallography and Mineral Physics,
Dept. = of=20 Geological=20 Sciences,          &nbs= p;            = ;            =          =20
University College=20 London,           =             &= nbsp;           &n= bsp;           &nb= sp;  =20
Gower=20 Street,           =             &= nbsp;           &n= bsp;           &nb= sp;           &nbs= p;          =20
London WC1E=20 6BT,           &nb= sp;           &nbs= p;            = ;            =            =20
U.K.           = ;            =             &= nbsp;           &n= bsp;           &nb= sp;           &nbs= p;            = ;=20
E-mail : a.oganov@ucl.ac.uk  &nbs= p;            = ;            =             &= nbsp;     =20
Tel. : +44 (0)171-419-3449        = Fax :=20 +44=20 (0)171-387-1612         &nbs= p;            = ;            =             &= nbsp;   
****************************************************************= ******
------=_NextPart_000_0033_01BF2A34.606EBFC0-- From chemistry-request@server.ccl.net Tue Nov 9 03:24:21 1999 Received: from gatekeeper.rp-rorer.co.uk ([195.232.82.242]) by server.ccl.net (8.8.7/8.8.7) with SMTP id DAA14843 for ; Tue, 9 Nov 1999 03:24:21 -0500 Received: from dagbh01.dag.rpr.rp (dagbh01.rp-rorer.co.uk) by gatekeeper.rp-rorer.co.uk with SMTP id IAA05522 (InterLock SMTP Gateway 4.2 for ); Tue, 9 Nov 1999 08:17:25 GMT Received: by dagbh01.dag.rpr.rp with Internet Mail Service (5.5.2448.0) id <44LA2Q5C>; Tue, 9 Nov 1999 08:17:23 -0000 Message-Id: <2217D24173C6D111849800008327F8EF013B3FB7@dagex01.dag.rpr.rp> From: "CLARK, David-E" To: "'Chemistry@ccl.net'" Subject: CCL: Genetic Algorithms in Chemistry Date: Tue, 9 Nov 1999 08:17:21 -0000 Mime-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: text/plain A regularly updated bibliography of evolutionary algorithm applications in CAMD can be found at: http://panizzi.shef.ac.uk/cisrg/links/ea_bib.html I would welcome any additions or corrections to the bibliography. Best wishes David David E. Clark, PhD Computer-Aided Drug Design Rhone-Poulenc Rorer Ltd. Dagenham Research Centre Rainham Road South Dagenham Essex RM10 7XS United Kingdom Tel: +44-181-919-3353 Fax: +44-181-919-2029 Email: david-e.clark@rp-rorer.co.uk