From chemistry-request@server.ccl.net Fri Apr 19 08:38:11 2002 Received: from albert.unito.it ([130.192.119.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3JCcAj01856 for ; Fri, 19 Apr 2002 08:38:11 -0400 Received: (from root@localhost) by albert.unito.it (8.12.2/8.12.2) id g3JCc294026117 for chemistry@ccl.net; Fri, 19 Apr 2002 14:38:02 +0200 Received: from unito.it (fpc24.pharm.unito.it [130.192.116.24]) by albert.unito.it (8.12.2/8.12.2) with ESMTP id g3JCc2Er026076 for ; Fri, 19 Apr 2002 14:38:02 +0200 Message-ID: <3CC01008.D07CDCD6@unito.it> Date: Fri, 19 Apr 2002 14:39:36 +0200 From: Giuseppe Ermondi X-Mailer: Mozilla 4.78 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Charge and Force field parametrization X-scanner: scanned by Inflex 1.0.9 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi CCL, I am working with Autodock and GROMACS and I am looking for articles, reviews or other material regarding two subjects: 1) how can evaluate charge distribution for molecules or groups like heme in order to obtain reasonable charges (coherent with "classical" sets like Amber or Kollman charges)? Are there any compilations of charges for uncommon groups? 2) how can obtain reasonable parametrization for the same groups? Are there databases available for the more usefull programs? Thank you Regards Giuseppe Ermondi _____________________________________________________________________ For your security, this mail has been scanned and protected by Inflex From chemistry-request@server.ccl.net Fri Apr 19 13:25:31 2002 Received: from TheWorld.com ([199.172.62.104]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3JHPVj08173 for ; Fri, 19 Apr 2002 13:25:31 -0400 Received: from world.std.com (dkeren@world-f.std.com [199.172.62.5]) by TheWorld.com (8.9.3/8.9.3) with ESMTP id NAA31919 for ; Fri, 19 Apr 2002 13:25:21 -0400 Received: (from jle@localhost) by world.std.com (8.9.3/8.9.3) id NAA17198 for chemistry@ccl.net; Fri, 19 Apr 2002 13:25:21 -0400 (EDT) Date: Fri, 19 Apr 2002 13:25:21 -0400 (EDT) From: Joe M Leonard Message-Id: <200204191725.NAA17198@world.std.com> To: chemistry@ccl.net Subject: Determining rotation angles from rotation matrix By any chance does anybody have code which determines the cartesian rotation angles from a rotation matrix? I need to pass the angles back into a GA calculation, and thought I'd ask CCL before disappearing off into trig-land for a while... I hate trig-land :-). I also hope that somebody's figured this out and can point me to it. My Google searches haven't been as fruitful as I'd like. Thanks in advance! Joe Leonard jle@theworld.com (formerly jle@world.std.com - ISP name change) From chemistry-request@server.ccl.net Fri Apr 19 19:48:32 2002 Received: from mxout3.cac.washington.edu ([140.142.32.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3JNmVA04054 for ; Fri, 19 Apr 2002 19:48:32 -0400 Received: from mailscan-out3.cac.washington.edu (mailscan-out3.cac.washington.edu [140.142.32.18]) by mxout3.cac.washington.edu (8.12.1+UW01.12/8.12.1+UW02.01) with SMTP id g3JNmI8J030162 for ; Fri, 19 Apr 2002 16:48:19 -0700 Received: FROM mailhost2.u.washington.edu BY mailscan-out3.cac.washington.edu ; Fri Apr 19 16:48:18 2002 -0700 Received: from donald ([128.95.128.116]) by mailhost2.u.washington.edu (8.12.1+UW01.12/8.12.1+UW02.01) with SMTP id g3JNmIww023155 for ; Fri, 19 Apr 2002 16:48:18 -0700 Message-ID: <009601c1e7fc$b4410760$74805f80@donald> From: "Carsten Detering" To: Subject: charges and database, multimol2 file Date: Sat, 20 Apr 2002 01:48:28 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0093_01C1E80D.77990360" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0093_01C1E80D.77990360 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CClers, I wounder if there is any other way in assigning charges/hydrogens to = molecules in a multimol2 or SDF database file, except from doing it with = SYBYL. Any suggestions are gladly appreciated! Thanks in advance, Carsten -------------------------------------------------- Carsten Detering,Ph.D University of Washington Department of Chemistry Bagley Hall, Box 351700 Seattle, WA 98195 detering@u.washington.edu ------=_NextPart_000_0093_01C1E80D.77990360 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear CClers,
 
I wounder if there is any other way in = assigning=20 charges/hydrogens to molecules in a multimol2 or SDF database file, = except=20 > from doing it with SYBYL.
Any suggestions are gladly=20 appreciated!
 
Thanks in advance,
 
Carsten
 
--------------------------------------------------
Carsten=20 Detering,Ph.D
University of Washington
Department of = Chemistry
Bagley=20 Hall, Box 351700
Seattle, WA 98195
detering@u.washington.edu
------=_NextPart_000_0093_01C1E80D.77990360-- From chemistry-request@server.ccl.net Fri Apr 19 23:13:57 2002 Received: from gate-sl1.mdli.com ([208.200.221.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3K3DvA06119 for ; Fri, 19 Apr 2002 23:13:57 -0400 Received: (from smap@localhost) by gate-sl1.mdli.com (8.8.8/8.8.8) id UAA22498; Fri, 19 Apr 2002 20:13:50 -0700 (PDT) Received: from puffin.mdli.com(172.16.1.12) by gate-sl1 via smap (V2.1) id xma022496; Fri, 19 Apr 02 20:13:46 -0700 Received: from blackbird.mdli.com by puffin.mdli.com (980427.SGI.8.8.8/BCH1.0) id UAA01248; Fri, 19 Apr 2002 20:13:45 -0700 (PDT) Received: from mdli.com (localhost [127.0.0.1]) by blackbird.mdli.com (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id UAA58779; Fri, 19 Apr 2002 20:13:44 -0700 (PDT) Sender: jdurant@mdli.com Message-ID: <3CC0DCE8.21C36397@mdli.com> Date: Fri, 19 Apr 2002 20:13:44 -0700 From: Joseph Durant X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: Carsten Detering , CCL Subject: Re: CCL:charges and database, multimol2 file References: <009601c1e7fc$b4410760$74805f80@donald> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Carsten, MDL's Cheshire scripting language is a possiblity. It ships with various SDfile scanning utilities, and a PEOE (sigma only) partial charge calculator based on Gasteiger's work is one of the example scripts. Implicit hydrogens are trivially obtainable except for transition metals where the valence evaluation becomes problematic. Joe > Carsten Detering wrote: > > Dear CClers, > > I wounder if there is any other way in assigning charges/hydrogens to > molecules in a multimol2 or SDF database file, except > from doing it with > SYBYL. > Any suggestions are gladly appreciated! > > Thanks in advance, > > Carsten > > -------------------------------------------------- > Carsten Detering,Ph.D > University of Washington > Department of Chemistry > Bagley Hall, Box 351700 > Seattle, WA 98195 > detering@u.washington.edu -- Joe Durant jdurant@mdli.com MDL Information Systems 14600 Catalina Street, San Leandro, CA 94577 voice: (510) 357-2222 x 1331 or (510) 895-1313 FAX: (510) 614-3616 -------------- "There are no stupid questions, but there are a lot of inquisitive idiots."