From chemistry-request@ccl.net Thu Aug 26 01:49:50 2004 Received: from mail1.cc.huji.ac.il (real-outmail.cc.huji.ac.il [132.64.1.17]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i7Q6nm8x013227 for ; Thu, 26 Aug 2004 01:49:49 -0500 Received: from localhost (localhost [127.0.0.1]) by mail1.cc.huji.ac.il (Postfix) with ESMTP id B519CAE358; Thu, 26 Aug 2004 09:58:25 +0300 (IDT) Received: from mail1.cc.huji.ac.il (localhost [127.0.0.1]) by localhost (VaMailArmor-2.0.1.16) id 07626-139C63BC; Thu, 26 Aug 2004 09:58:25 +0300 Received: by mail1.cc.huji.ac.il (Postfix, from userid 31998) id A9DAEAE7BD; Thu, 26 Aug 2004 09:58:25 +0300 (IDT) Received: from pob.huji.ac.il (pob.huji.ac.il [132.64.1.8]) by mail1.cc.huji.ac.il (Postfix) with ESMTP id 5A5C8AE358; Thu, 26 Aug 2004 09:58:25 +0300 (IDT) Received: by pob.huji.ac.il (Postfix, from userid 1673) id 9DDF7FB58; Thu, 26 Aug 2004 09:58:24 +0300 (IDT) Received: from localhost (localhost [127.0.0.1]) by pob.huji.ac.il (Postfix) with SMTP id 8DF9EFB54; Thu, 26 Aug 2004 09:58:24 +0300 (IDT) Date: Thu, 26 Aug 2004 09:58:24 +0300 (IDT) From: boris gorelik To: john Cc: chemistry)at(ccl.net Subject: Re: CCL:Converting cartesian gradients to Z-matrix gradients In-Reply-To: <412C3C15.100D3967)at(attglobal.net> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Level: X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On Wed, 25 Aug 2004, john wrote: > Folks, > > I am looking convert a set of cartesian gradients into internal > gradients in a Z-matrix format. I do have the Z-matrix form of the > corresponding cartesian coordinates.. openbabel can convert between lots of formatst (pdb, mol2, xyz, etc etc). one of the supported output format is fh, which is Fenske-Hall ZMatrix file (which holds the internal coordinates of the molecule). Unfortunately it does not convert into opposite direction. I have some functions (C++) that convert between internal and cortesian coordinates. Contact me off the list if you want them > > Any suggesstions as to where some code to do this would be most > appreciated. > > Many thanks for your suggestions! > > John McKelvey > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY)at(ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST)at(ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski,jlabanow)at(nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Thu Aug 26 10:04:07 2004 Received: from duras.rz-berlin.mpg.de (duras.RZ-Berlin.MPG.DE [141.14.130.154]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i7QF46UJ021554 for ; Thu, 26 Aug 2004 10:04:06 -0500 Received: from localhost (unknown [127.0.0.1]) by duras.rz-berlin.mpg.de (Postfix) with ESMTP id 92AEFED3BF; Thu, 26 Aug 2004 17:12:52 +0200 (CEST) Received: from duras.rz-berlin.mpg.de ([127.0.0.1]) by localhost (duras [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 51681-06; Thu, 26 Aug 2004 17:12:50 +0200 (CEST) Received: from [141.14.128.99] (mdg5.RZ-Berlin.MPG.DE [141.14.128.99]) by duras.rz-berlin.mpg.de (Postfix) with ESMTP id D2E2AED35F; Thu, 26 Aug 2004 17:12:50 +0200 (CEST) In-Reply-To: References: Mime-Version: 1.0 (Apple Message framework v619) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Message-Id: <67485B9F-F772-11D8-95BF-000A95A7C604*at*fhi-berlin.mpg.de> Content-Transfer-Encoding: 7bit Cc: CHEMISTRY*at*ccl.net From: Gert von Helden Subject: Re: CCL:Gaussian03 on G5 dual Date: Thu, 26 Aug 2004 17:12:53 +0200 To: Dai Hibbs X-Mailer: Apple Mail (2.619) X-Virus-Scanned: by amavisd-new (PP&B) at duras Hi, I compiled g03 with IBM's xlf 8.1 compiler on a 2 GHz G5, MacOSX 10.3.5. Some adjustments in the makefile and in some machine dependent code was necessary. The exe is 32 bit and it runs on 1 processor only (with some more effort, one should be able to compile it for two - i did not bother). I ran an (arbitrary) benchmark, an large MP2 frequency calc. It runs on a 2 GHz G5 20 % faster than on a 2.2 GHz Opteron (32 bit mode) and 2.5 times faster than on a 2 GHz Xeon. You can have single rwf files of 16 GB (the 32 bit limit). I would expect that the next official g03 minor release will support the G5, as the port is easy and I did not (yet) find any bugs. Greetings, Gert On Aug 25, 2004, at 7:11 AM, Dai Hibbs wrote: > Hi all, > > This is probably a question that has been asked and answered many > times, > but has anyone had any success at getting G03 running and optimized on > a > MacG5 dual? > > Any advice re: compilers, makefile or code changes would be greatly > appreciated. > > Many Thanks > Dai > > *********************************************************************** > ******* > Dai Hibbs Phone: (61)-2-9036 9122 > School of Chemistry Fax: (61)-2-9351 3329 > University of Sydney e-mail: > d.hibbs*at*chem.usyd.edu.au > NSW 2006 > Australia > www.chem.usyd.edu.au > *********************************************************************** > ******* > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line > and send your message to: CHEMISTRY*at*ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST*at*ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow*at*nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+ > > > > > > ------------------------------------- Gert von Helden Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4-6 14195 Berlin tel.: +49-30-8413 5615 fax: +49-30-8413 5603 From chemistry-request@ccl.net Thu Aug 26 20:37:19 2004 Received: from mhub-m4.tc.umn.edu (mhub-m4.tc.umn.edu [160.94.23.34]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i7R1bIq2010670 for ; Thu, 26 Aug 2004 20:37:19 -0500 Received: from uvigo.es (CPE-24-163-205-16.mn.rr.com [24.163.205.16] (may be forged)) by mhub-m4.tc.umn.edu with ESMTP for CHEMISTRY(at)ccl.net; Thu, 26 Aug 2004 20:46:09 -0500 (CDT) X-Umn-Remote-Mta: [N] CPE-24-163-205-16.mn.rr.com [24.163.205.16] #+HF+TS+AU Message-ID: <412EAFB9.4030900(at)uvigo.es> Date: Thu, 26 Aug 2004 20:51:21 -0700 From: Carlos Silva Lopez User-Agent: Mozilla Thunderbird 0.5 (X11/20040208) X-Accept-Language: en-us, en MIME-Version: 1.0 To: CHEMISTRY(at)ccl.net Subject: SUMMARY: One negative eigenvalue - No imaginary frequency!!?? Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=2.4 required=7.5 tests=PLING_QUERY,RCVD_IN_DYNABLOCK, RCVD_IN_SORBS,SMILEY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi CCLers, I have already received a good number of suggestions, I would like to thank specially Per-Ola Norrby, J. Fox (gaussian support), Steve Williams, Shaji chempath and Anastassia Alexandrova (I hope I am not forgetting anybody). Some of the suggestions doubted my skills to reach a stationary point on the PES ;-) actually that had been my first guess and I tightened the convergence criteria of the SCF and the optimization to the maximum, I also used an uncommonly fine integration mesh. So, yes, I am at a stationary point (well, the structure is, to be rigourous). Actually I re-started the calculation until I got a converged structure with null forces (at the precision level of the gaussian output, of course) in the frequency job. Other suggestions were to employ more robust methods for this particular serching (QST2,QST3,Nudged Elastic Band). I tried the first two methods with no better luck. Another person pointed out that gaussian might sometimes interchange the last rotation/vibration with the first vibration. I am not sure about how to check this, but it looks like a possibility due to my lasts trials (see below). Several suggestions pointed that my calculation was not reaching close enough to the TS or reaching a shallow minimum instead. As I said I am defenitely at a stationary point (from the ultra low forces and displacements I got) but if I take this converged structure and run it to converge to a minimum....surprise!!!! it goes off towards the "real" minimum of the products of the nucleophilic attack. In a nutshell, I am even more clueless than before even though I have received really nice and welcomed help from several netters. If nobody has any further idea about what's going on here I will eventually re-converge everything within a continuum dielectric method to see if it counterbalances the anionic charge state and everything goes better. Thanks so much to everybody supporting this list! From chemistry-request@ccl.net Thu Aug 26 14:30:16 2004 Received: from web53306.mail.yahoo.com (web53306.mail.yahoo.com [206.190.39.235]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i7QJUFYt010810 for ; Thu, 26 Aug 2004 14:30:15 -0500 Message-ID: <20040826193902.20051.qmail-.at.-web53306.mail.yahoo.com> Received: from [130.74.167.153] by web53306.mail.yahoo.com via HTTP; Thu, 26 Aug 2004 12:39:02 PDT Date: Thu, 26 Aug 2004 12:39:02 -0700 (PDT) From: prashant desai Subject: Lynux based hardware for GOLD To: chemistry-.at.-ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-555090771-1093549142=:17713" X-Spam-Status: No, hits=5.0 required=7.5 tests=FROM_ENDS_IN_NUMS,HTML_20_30, HTML_MESSAGE,MK_BAD_HTML_04,MK_YAHOO_REDIR_01,WLS_URI_OPT_150 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --0-555090771-1093549142=:17713 Content-Type: text/plain; charset=us-ascii I am looking for some powerful lynux based machines (servers/clusters etc) for running GOLD docking program. Any suggestions/comments based on your experience? Thanks. Dr. Prashant Desai --------------------------------- Do you Yahoo!? Yahoo! Mail - You care about security. So do we. --0-555090771-1093549142=:17713 Content-Type: text/html; charset=us-ascii
I am looking for some powerful lynux based machines (servers/clusters etc) for running GOLD docking program. Any suggestions/comments based on your experience?
 
Thanks.
 
Dr. Prashant Desai

Do you Yahoo!?
Yahoo! Mail - You care about security. So do we. --0-555090771-1093549142=:17713-- From chemistry-request@ccl.net Thu Aug 26 15:48:08 2004 Received: from mail.fq.edu.uy (mail.fq.edu.uy [164.73.160.197]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i7QKm5q2017475 for ; Thu, 26 Aug 2004 15:48:06 -0500 Received: from CHAGASPACE2 (chagaspace2.fq.edu.uy [164.73.161.9]) by mail.fq.edu.uy (8.12.8/8.12.4) with SMTP id i7QKuct7008371 for ; Thu, 26 Aug 2004 17:56:53 -0300 Message-ID: <01dc01c48baf$3706d9b0$09a149a4@CHAGASPACE2> From: "Federico Iribarne" To: Subject: LIE and GROMOS96 Date: Thu, 26 Aug 2004 17:56:40 -0300 Organization: =?iso-8859-1?Q?Facultad_de_Qu=EDmica?= MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_01D9_01C48B96.0A1107A0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1437 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1441 X-Scanned-By: MIMEDefang 2.29 (www . roaringpenguin . com / mimedefang) X-Spam-Status: No, hits=1.0 required=7.5 tests=HTML_30_40,HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_01D9_01C48B96.0A1107A0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello, Has someone been able to successfully apply the LIE method for = estimation of binding free energies using the GROMOS96 simulation = package? I am studying the binding of some charged ligands to enzyme receptors = but it seems there=B4s a problem with the description of molecular = interactions (specially electrostatic) since the results are nowhere = near the experimental ones. I am using solvated spheres with the extended wall boundary condition = and a 17 A cut off radius for long range non bonded interactions. A = reaction field correction is applied to account for the missing = electrostatic contributions outside the sphere. I could not find any papers where something like this was attempted = (i.e., LIE combined with GROMOS96). I am aware the Q program is out there but I just would like to make it = right using GROMOS96. Any pointers will be greatly appreciated. Thanks, F. ------=_NextPart_000_01D9_01C48B96.0A1107A0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello,
 
Has someone been able to successfully = apply the LIE=20 method for estimation of binding free energies using the GROMOS96 = simulation=20 package?
 
I  am studying the binding of some = charged=20 ligands to enzyme receptors but it seems there=B4s a problem with the = description=20 of molecular interactions (specially electrostatic) since the results = are=20 nowhere near the experimental ones.
 
I am using solvated spheres with the = extended wall=20 boundary condition and a 17 A cut off radius for long range non bonded=20 interactions. A reaction field correction is applied to = account for=20 the missing electrostatic contributions outside the sphere.
 
I could not find any papers where = something like=20 this was attempted (i.e., LIE combined with GROMOS96).
 
I am aware the Q program is out there = but I just=20 would like to make it right using GROMOS96.
 
Any pointers will be greatly=20 appreciated.
 
Thanks,
F.
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