From chemistry-request@server.ccl.net Fri Dec 20 00:35:26 2002 Received: from mailpost2.aist-nara.ac.jp ([163.221.80.22]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBK5ZQi05654 for ; Fri, 20 Dec 2002 00:35:26 -0500 Received: from mailgate.aist-nara.ac.jp (mailgate.aist-nara.ac.jp [163.221.80.65]) by mailpost2.aist-nara.ac.jp (Postfix) with SMTP id C3CC2E2C37 for ; Fri, 20 Dec 2002 14:35:25 +0900 (JST) Received: (qmail 5056 invoked from network); 20 Dec 2002 14:35:24 +0900 Received: from viruscan.aist-nara.ac.jp (HELO tungstenn) (163.221.80.60) by mailgate.aist-nara.ac.jp with SMTP; 20 Dec 2002 14:35:24 +0900 Message-ID: <000e01c2a7e9$98545f40$5f60dda3@tungstenn> From: "dakshanamurthy sivanesan" To: Subject: Low electrostatic energy obtained in Delphi Date: Fri, 20 Dec 2002 14:35:24 +0900 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000B_01C2A835.081397B0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 Disposition-Notification-To: "dakshanamurthy sivanesan" X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 This is a multi-part message in MIME format. ------=_NextPart_000_000B_01C2A835.081397B0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCLers: Happy New Year to all! I did calculate electrostatic energy for several proteins to look at = protein-ligand interactions using Delphi in INSIGHT2000. I got low = electrostatic energy (obtained using ESP and AMBER partial charges) = which lies in the range around 0.5 to 1 Kcal/mol.=20 Could anybody explain the reason for why is it so low. Thanks in advance! sincerely, Siva=20 ------=_NextPart_000_000B_01C2A835.081397B0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear CCLers:
Happy New Year to all!

I did calculate = electrostatic=20 energy for several proteins to look at protein-ligand interactions using = Delphi=20 in INSIGHT2000. I got low electrostatic energy (obtained using ESP and = AMBER=20 partial charges) which lies in the range around 0.5 to 1 Kcal/mol. =

Could=20 anybody explain the reason for why is it so low.

Thanks in=20 advance!

sincerely,
Siva

------=_NextPart_000_000B_01C2A835.081397B0-- From chemistry-request@server.ccl.net Fri Dec 20 04:45:11 2002 Received: from gate3.oss.akzonobel.nl ([192.87.3.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBK9jAi22239 for ; Fri, 20 Dec 2002 04:45:10 -0500 Received: (from fwmaster@localhost) by gate3.oss.akzonobel.nl (8.9.3a/8.6.12) id KAA22873 for ; Fri, 20 Dec 2002 10:45:10 +0100 (MET) Received: by gate3.oss.akzonobel.nl via smap (V1.3) id sma013213; Fri, 20 Dec 02 10:37:04 +0100 Received: by triton.oss.intra with Internet Mail Service (5.5.2653.19) id ; Fri, 20 Dec 2002 10:37:04 +0100 Message-ID: <639D20177889D41198A600508BAD3CA1039AD2DD@capella3.oss.akzonobel.nl> From: "Lommerse, J.P.M. (Jos)" To: "'chemistry@ccl.net'" Cc: "Vuuren, M. van (Marlous)" Subject: Constrained geometry optimisation with GAUSSIAN98 Date: Fri, 20 Dec 2002 10:37:00 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Hello, I am trying to optimize the geometry of small organic molecules while keeping fixed all dihedral angles at certain values around rotatable bonds. Whatever optimization procedure (Berny, Steep, etc.) I apply, or start conformation I choose, the optimization fails to arrive at a true local minimum, viz. the resulting geometry always contains one or more imaginary frequencies. Does anybody know how to get to a true local minimum while applying these dihedral angle constraints? Here's an simple problem molecule example com-file for GAUSSIAN98 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ %chk=pdb35.chk # rhf/PM3 Molecule pdb35 (1isi_NCA_1) 0 1 N 6.3300 42.5360 90.0450 C 5.1180 41.9260 90.5820 C 3.9970 42.7130 90.9900 C 4.1850 44.1520 90.8210 C 5.3590 44.7550 90.2990 C 6.4330 43.9350 89.9100 C 2.6760 42.1220 91.5670 O 1.7720 42.8950 91.8870 N 2.5360 40.8370 91.7060 H 5.0663 40.8412 90.6744 H 3.3664 44.8083 91.1165 H 5.4271 45.8385 90.2010 H 7.3421 44.3799 89.5054 H 3.3010 40.2032 91.4339 H 1.6602 40.4528 92.0883 --Link1-- %chk=pdb35.chk #T rhf/PM3 geom=(checkpoint,modify) opt=modredundant * * A * * * A * * * * A * 3 7 * F ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Thanks a lot, Jos Lommerse jos.lommerse@organon.com Dr Ir Jos Lommerse, Research Scientist Molecular Design & Informatics, N.V. Organon Molenstraat 110, PO Box 20, 5340 BH Oss, THE NETHERLANDS -------------------------------------------------------------------- This message, including attached files, may contain confidential information and is intended only for the use by the individual and/or the entity to which it is addressed. Any unauthorized use, dissemination of, or copying of the information contained herein is not allowed and may lead to irreparable harm and damage for which you may be held liable. If you receive this message in error or if it is intended for someone else please notify the sender by returning this e-mail immediately and delete the message. -------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Dec 20 09:24:52 2002 Received: from gip2.u-picardie.fr ([193.49.184.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBKEOpi28387 for ; Fri, 20 Dec 2002 09:24:51 -0500 Received: by gip2.u-picardie.fr (Postfix, from userid 33) id 011569239; Fri, 20 Dec 2002 15:24:50 +0100 (CET) To: chemistry@ccl.net, pdb-l@sdsc.edu Subject: Looking for a program Message-ID: <1040394290.3e032832e8f3a@webmail.u-picardie.fr> Date: Fri, 20 Dec 2002 15:24:50 +0100 (CET) From: FyD MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.6 Dear All, I am looking for a program that: 1- Would work under UNIX (in particular Linux & Irix), 2- Could be ran using scripts i.e. in a non-graphical way, 3- Would allow to (i) load a structure, (ii) modify/control its orientation (axis x, y, and z), and (iii) save the new Cartesian coordinate set defined by the new orientation, and if possible 4- would be freely distributed for all users... Thanks, Regards, Francois From chemistry-request@server.ccl.net Fri Dec 20 11:02:15 2002 Received: from mercury.sunesis.com ([64.240.200.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBKG2Ei30154 for ; Fri, 20 Dec 2002 11:02:15 -0500 Received: from penguin.sunesis.com ([192.168.1.63]) by mercury.sunesis.com with Microsoft SMTPSVC(5.0.2195.2966); Fri, 20 Dec 2002 08:02:11 -0800 Date: Fri, 20 Dec 2002 08:02:11 -0800 (PST) From: "Warren L. DeLano" To: FyD cc: Subject: Re: CCL:Looking for a program In-Reply-To: <1040394290.3e032832e8f3a@webmail.u-picardie.fr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-OriginalArrivalTime: 20 Dec 2002 16:02:11.0527 (UTC) FILETIME=[27E22D70:01C2A841] Francois, try PYMOL! http://pymol.sf.net 1) runs under linux, irix, windows, osx 2) command mode available with "pymol -c" 3i) reads and writes PDB, SDF, MOL, etc. 3ii) transformation can be done with mouse or explicit "translate", "rotate" commands as well as a combined sequence/structure alignment "align" command. 3iii) "save filename.pdb" will store your new coordinates 4) PyMOL is free, modifiable, and redistributable in modified form. I (the author) do make periodic requests for funding to support ongoing development, but such funding remains optional. Before too long, I'll be rewarding such support with a feature-enhanced version. Cheers, Warren On Fri, 20 Dec 2002, FyD wrote: > Dear All, > > I am looking for a program that: > 1- Would work under UNIX (in particular Linux & Irix), > 2- Could be ran using scripts i.e. in a non-graphical way, > 3- Would allow to (i) load a structure, (ii) modify/control its orientation > (axis x, y, and z), and (iii) save the new Cartesian coordinate set defined by > the new orientation, and if possible > 4- would be freely distributed for all users... > > Thanks, Regards, Francois From chemistry-request@server.ccl.net Fri Dec 20 13:18:44 2002 Received: from gip2.u-picardie.fr ([193.49.184.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBKIIhi31895 for ; Fri, 20 Dec 2002 13:18:43 -0500 Received: by gip2.u-picardie.fr (Postfix, from userid 33) id DCA9B923B; Fri, 20 Dec 2002 19:18:43 +0100 (CET) To: chemistry@ccl.net, pdb-l@sdsc.edu Subject: Looking for a program_II Message-ID: <1040408323.3e035f03cfedb@webmail.u-picardie.fr> Date: Fri, 20 Dec 2002 19:18:43 +0100 (CET) From: FyD References: <1040394290.3e032832e8f3a@webmail.u-picardie.fr> <3E0355DF.6070505@lbl.gov> In-Reply-To: <3E0355DF.6070505@lbl.gov> MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.6 Dear Edward Berry, Dear All, > How do you want to specify the 'modification of orientation' > in a non-graphical program? If you can specify a rotation > matrix or rotation angle about an axis defined > by direction cosines, or a series of rotations about > principal axes, then this is a very simple program. > pdbset (CCP4) or moleman (USF) do this and much more, > and are free to academic users. Otherwise they meet > your criteria. I get a lot of answers with graphical rotation controls using the mouse: I think I have to explain how I "would like/need" to control the orientation of my structure: I am NOT interested in controlling the orientation of my structures using the mouse, i.e. I am NOT interested in a graphical control but I would like to control the orientation using for instance atom names (in a script): - I would like first to put the center of mass at 0, 0, 0 - Then, select 2 atom names "A", "B" to define the O -> x axis and a third one, "C" to define the plane o, x, y. Then, apply the rotation as previously defined and save the structure to 'a' format. - I would also be interested in any other non-graphical reorientation procedure. The idea is simply to have 'a' control of the structure orientation. I also forgot to tell you that I need to load an input structure at a format allowing at least 4 digits after the decimal points and obviously to save the ouput reoriented structure with these same 4 digits. It means PDB format can be used but the saved structure must be writen with these 4 digits. Another solution are the sybyl or xyz formats. Thanks, regards, Francois From chemistry-request@server.ccl.net Fri Dec 20 19:59:57 2002 Received: from ns0.scripps.edu ([192.42.82.58]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBL0xui03840 for ; Fri, 20 Dec 2002 19:59:56 -0500 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns0.scripps.edu (8.11.6/TSRI-4.2rx) with SMTP id gBL0xuL29356 for ; Fri, 20 Dec 2002 16:59:56 -0800 (PST) Received: from relay1.scripps.edu(137.131.200.29) by antigen.scripps.edu via csmap id 27098; Fri, 20 Dec 2002 16:55:29 -0800 (PST) Received: from gamow.scripps.edu (gamow.scripps.edu [137.131.252.67]) by relay1.scripps.edu (8.11.6/TSRI-4.2.1rAV) with ESMTP id gBL0xpA05283 for ; Fri, 20 Dec 2002 16:59:51 -0800 (PST) Received: from quine.scripps.edu (quine [137.131.252.41]) by gamow.scripps.edu (8.9.2/TSRI-3.0.1) with SMTP id QAA161155 for ; Fri, 20 Dec 2002 16:59:50 -0800 (PST) Received: by quine.scripps.edu (sSMTP sendmail emulation); Fri, 20 Dec 2002 16:59:48 -0800 Date: Fri, 20 Dec 2002 16:59:48 -0800 From: "David A. Case" To: chemistry@ccl.net Subject: Re: CCL:Looking for a program for orienting molecules Message-ID: <20021221005948.GB1576@scripps.edu> References: <1040394290.3e032832e8f3a@webmail.u-picardie.fr> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <1040394290.3e032832e8f3a@webmail.u-picardie.fr> User-Agent: Mutt/1.4i On Fri, Dec 20, 2002, FyD wrote: > > I am looking for a program that: > 1- Would work under UNIX (in particular Linux & Irix), > 2- Could be ran using scripts i.e. in a non-graphical way, > 3- Would allow to (i) load a structure, (ii) modify/control its orientation > (axis x, y, and z), and (iii) save the new Cartesian coordinate set defined by > the new orientation, and if possible > 4- would be freely distributed for all users... > The NAB program (see the web site below) was designed to do exactly this, serving as sort of a "molecular awk". It is pretty much limited to reading and writing pdb-format files (e.g. no mol2, cif, etc). In spite of its name (Nucleic Acid Builder), it is not restricted to nucleic acids, and I use it for the above purposes all the time. It is licensed under the GPL, and should work on Linux, BSD, most Unices, cygwin and Mac OS X. ..hope this helps...dac -- ================================================================== David A. Case | e-mail: case@scripps.edu Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | http://www.scripps.edu/case ================================================================== From chemistry-request@server.ccl.net Fri Dec 20 22:20:20 2002 Received: from prserv.net ([32.97.166.32]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBL3KKi04566 for ; Fri, 20 Dec 2002 22:20:20 -0500 Received: from attglobal.net (slip-12-64-60-104.mis.prserv.net[12.64.60.104]) by prserv.net (out2) with SMTP id <2002122103201820200fbqgqe>; Sat, 21 Dec 2002 03:20:20 +0000 Message-ID: <3E03988B.9018D299@attglobal.net> Date: Fri, 20 Dec 2002 22:24:12 +0000 From: jmmckel@attglobal.net Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Looking for a program to clean Fortran Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit CCLers, I have some Fortran code that desperately needs cleaning up. Is there any free/inexpensive software available to do this? Thanks! John McKelvey