From chemistry-request@ccl.net Thu Jan 13 11:07:03 2005 Received: from sandmail01.sd.accelrys.com (rrcs-67-52-158-62.west.biz.rr.com [67.52.158.62]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0DG71qd007929; Thu, 13 Jan 2005 11:07:01 -0500 In-Reply-To: To: leif.olson{at}kodak.com Cc: chemistry{at}ccl.net, "Computational Chemistry List" Subject: Re: CCL:Silver NMR shifts using PBC MIME-Version: 1.0 X-Mailer: Lotus Notes Release 6.5.2 June 01, 2004 Message-ID: From: George Fitzgerald Date: Thu, 13 Jan 2005 08:06:57 -0800 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 6.5.2|June 01, 2004) at 01/13/2005 08:06:59 AM, Serialize complete at 01/13/2005 08:06:59 AM Content-Type: multipart/alternative; boundary="=_alternative 005885FF88256F88_=" X-Spam-Status: No, hits=1.3 required=7.5 tests=HTML_20_30,HTML_MESSAGE, MK_BAD_HTML_04 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 multipart message in MIME format. --=_alternative 005885FF88256F88_= Content-Type: text/plain; charset="US-ASCII" Dear Lief, Accelrys offers the program NMR CASTEP for computing NMR chemical shifts and electric field gradient tensors for solid-state systems. You can find more information on our web site at http://www.accelrys.com/mstudio/ms_modeling/nmrcastep.html. The underlying method is similar to that implemented in PARATEC. The CASTEP interface, however, makes the implementation very easy to use. I will contact you privately with additional information. Sincerley, George Fitzgerald George Fitzgerald, Ph.D. gxf{at}accelrys.com Accelrys, Inc. Tel: +1 858 799 5360 10188 Telesis Court Fax: +1 858 799 5100 Suite 100 Mobile: +1 858 692 8722 San Diego, CA 92121 leif.olson{at}kodak.com Sent by: "Computational Chemistry List" 01/12/2005 11:37 AM To chemistry{at}ccl.net cc Subject CCL:Silver NMR shifts using PBC Hello CCL, I want to compute the Ag-109 chemical shifts in a crystal structure, using periodic boundary conditions if possible. The idea is to determine how an X-ray structure and a CP-MAS Ag-109 spectrum compare to each other. I've done NMR computations before (and a few PBC calculations using Gaussian 03) but only a few PBC calculations using software that was actually designed primarily for the solid state. Attempted NMR calculations using Gaussian 03 with PBC did not work. After poking around the Internet and the literature a bit, it seems that a couple of programs that might do what I want are PARATEC and CPMD. But the PARATEC website states "This code is primarily intended for users who are familiar with the plane-wave pseudopotential method used in PARATEC". Hmmm. The CPMD site doesn't say anything like that, but it does seem to be designed primarily for molecular dynamics simulations. Advice on these or other programs that might be appropriate would be appreciated. Thanks, Leif Olson Eastman Kodak Research Laboratories leif.olson{at}kodak.com --=_alternative 005885FF88256F88_= Content-Type: text/html; charset="US-ASCII"
Dear Lief,

Accelrys offers the program NMR CASTEP  for computing NMR chemical shifts and electric field gradient tensors for solid-state systems. You can find more information on our web site at http://www.accelrys.com/mstudio/ms_modeling/nmrcastep.html. The underlying method is similar to that implemented in PARATEC. The CASTEP interface, however, makes the implementation very easy to use.

I will contact you privately with additional information.

Sincerley,
George Fitzgerald


George Fitzgerald, Ph.D.       gxf{at}accelrys.com
Accelrys, Inc.                             Tel:  +1 858 799 5360
10188 Telesis Court                 Fax: +1 858 799 5100
Suite 100                                     Mobile: +1 858 692 8722
San Diego, CA 92121


leif.olson{at}kodak.com
Sent by: "Computational Chemistry List" <chemistry-request{at}ccl.net>

01/12/2005 11:37 AM

To
chemistry{at}ccl.net
cc
Subject
CCL:Silver NMR shifts using PBC






Hello CCL,

I want to compute the Ag-109 chemical shifts in a crystal structure, using periodic boundary conditions if possible.  The idea is to determine how an X-ray structure and a CP-MAS Ag-109 spectrum compare to each other.

I've done NMR computations before (and a few PBC calculations using Gaussian 03) but only a few PBC calculations using software that was actually designed primarily for the solid state.  Attempted NMR calculations using Gaussian 03 with PBC did not work.

After poking around the Internet and the literature a bit, it seems that a couple of programs that might do what I want are PARATEC and CPMD.  But the PARATEC website states "This code is primarily intended for users who are familiar with the plane-wave pseudopotential method used in PARATEC".  Hmmm.  The CPMD site doesn't say anything like that, but it does seem to be designed primarily for molecular dynamics simulations.

Advice on these or other programs that might be appropriate would be appreciated.  

Thanks,

Leif Olson
Eastman Kodak Research Laboratories
leif.olson{at}kodak.com
--=_alternative 005885FF88256F88_=-- From chemistry-request@ccl.net Fri Jan 14 03:50:51 2005 Received: from mta1.sucs.soton.ac.uk (mta1.sucs.soton.ac.uk [152.78.128.140]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0E8onII025842 for ; Fri, 14 Jan 2005 03:50:50 -0500 Received: from [152.78.196.193] (scarlet.chem.soton.ac.uk [152.78.196.193]) (authenticated bits=0) by mta1.sucs.soton.ac.uk (8.12.10/8.12.10) with ESMTP id j0E8ohmb017632 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NO) for ; Fri, 14 Jan 2005 08:50:44 GMT Message-ID: <41E787DE.8000701$at$soton.ac.uk> Date: Fri, 14 Jan 2005 08:50:38 +0000 From: Luca Fenu Reply-To: l.a.fenu$at$soton.ac.uk Organization: university of southampton User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.7) Gecko/20040616 MultiZilla/1.6.4.0b X-Accept-Language: it, en-us, en MIME-Version: 1.0 To: chemistry$at$ccl.net Subject: Re: CCL:assigning protonation states References: <41E6413F.1000106$at$soton.ac.uk> In-Reply-To: <41E6413F.1000106$at$soton.ac.uk> X-Enigmail-Version: 0.84.2.0 X-Enigmail-Supports: pgp-inline, pgp-mime Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-ISS-MailScanner: Believed to be clean X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_COST autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Ok, here's what I got back. as many of you seemed to think this was a question of general interest, I prepared a little digest of all replies: Original Question: Luca Fenu wrote: > Dear CClers > > I'm looking for some program able to automatically (and reliably) > assign protonation states at Phisiological pH to small organic > molecules, preferably saved as mol2 files. As I can expect my boss > ranting if he's to shed any money for it, any freeware alternative > would be more than welcome. Any suggestion? many thanks > > luca Answers: > George Vacek wrote: > >> Luca, > > >> Among numerous other capabilities, QuacPac reliably enumerates pKa >> states for pH 2-14 (and outputs a variety of file formats). Check >> out http://www.eyesopen.com/products/applications/quacpac.html >> >> Most academics qualify to use OpenEye software at no charge. For >> more information on our philosophy concerning academics, please read >> http://www.eyesopen.com/business/licensing/commercial.html >> http://www.eyesopen.com/support/misc/letter_to_academics.html >> >> Regards, George Vacek >> >> VP, Business Development OpenEye Scientific Software >> vacek$at$eyesopen.com 505.473.7385 > thanks George... -- > PRODRG http://davapc1.bioch.dundee.ac.uk/prodrg > > does this > > Daan > yes, apparently it does. thanks Daan. -- > I think joelib.sf.net can do that. > > Egon > ditto. check the JOEpHModel(http://www-ra.informatik.uni-tuebingen.de/software/joelib/api/joelib/data/JOEPhModel.html) That's it. many thanks to everyone who answered Luca -- Real programmers don't comment! It was hard to write, It should be hard to read! From chemistry-request@ccl.net Thu Jan 13 11:34:34 2005 Received: from www.eyesopen.com (eyesopen.com [208.41.78.163]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0DGYXqd010078 for ; Thu, 13 Jan 2005 11:34:33 -0500 Received: from eyesopen.com (208-41-78-162.client.dsl.net [208.41.78.162]) (authenticated) by www.eyesopen.com (8.11.6/8.11.6) with ESMTP id j0DEv9J31148; Thu, 13 Jan 2005 07:57:09 -0700 Message-ID: <41E6A310.7000904^at^eyesopen.com> Date: Thu, 13 Jan 2005 09:34:24 -0700 From: George Vacek Organization: OpenEye Scientific Software User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Luca Fenu CC: chemistry^at^ccl.net Subject: Re: CCL:assigning protonation states References: <41E6413F.1000106^at^soton.ac.uk> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=1.9 required=7.5 tests=MY_DSL,NO_COST autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Luca, > I'm looking for some program able to automatically (and reliably) assign protonation states at Phisiological pH to small organic molecules, preferably saved as mol2 files. As I can expect my boss ranting if he's to shed any money for it, any freeware alternative would be more than welcome. Any suggestion? many thanks Among numerous other capabilities, QuacPac reliably enumerates pKa states for pH 2-14 (and outputs a variety of file formats). Check out http://www.eyesopen.com/products/applications/quacpac.html Most academics qualify to use OpenEye software at no charge. For more information on our philosophy concerning academics, please read http://www.eyesopen.com/business/licensing/commercial.html http://www.eyesopen.com/support/misc/letter_to_academics.html Regards, George Vacek VP, Business Development OpenEye Scientific Software vacek^at^eyesopen.com 505.473.7385 ********************************************************************* OpenEye recently announced the following software releases: EON 1.0, WABE 1.3, QUAC PAC 1.1, OMEGA 1.8, FRED 2.0 http://www.eyesopen.com/about/news/press_releases/ ********************************************************************* From chemistry-request@ccl.net Fri Jan 14 08:11:40 2005 Received: from mail2.qmul.ac.uk (mail2.qmul.ac.uk [138.37.6.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0EDBdII006496 for ; Fri, 14 Jan 2005 08:11:39 -0500 Received: from smtp.qmul.ac.uk ([138.37.6.40]) by mail2.qmul.ac.uk with esmtp (Exim 4.43) id 1CpREn-000105-Tg for CHEMISTRY!at!ccl.net; Fri, 14 Jan 2005 13:11:38 +0000 Received: from mmm1.mats.qmul.ac.uk ([138.37.43.102] helo=mmm1) by smtp.qmul.ac.uk with smtp (Exim 4.34) id 1CpREn-0001eY-Pf for CHEMISTRY!at!ccl.net; Fri, 14 Jan 2005 13:11:37 +0000 Message-ID: <003501c4fa3c$1febdef0$662b258a@mmm1> From: "Ru-Zhen Li" To: References: <41C9745E.302!at!chemaxon.com> Subject: compiling problems Date: Fri, 14 Jan 2005 13:22:41 -0000 MIME-Version: 1.0 Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=response Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2900.2180 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 X-Sender-Host-Address: 138.37.43.102 X-QM-Scan-Virus: virusscan says the message is clean X-QM-Scan-Virus: ClamAV says the message is clean X-Spam-Status: No, hits=5.0 required=7.5 tests=NO_RDNS2,WLS_URI_OPT_76 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear all, I am compiling some software with MPI, and the command is: $(MAKE) LD="ifort -o" \ LDFLAGS="-L/usr/local/encap/mpich-125-2-intel/lib -lmpich -lpmpich" \ FC=ifort FFLAGS="-c -O -B100" TIMER="" \ CPFLAGS="-D$(STRESS) -DMPI -P -D'POINTER=integer' \ -I/usr/local/encap/mpich-125-2-intel/include/" \ EX=$(EX) BINROOT=$(BINROOT) $(TYPE) during the compilation, the source file .f are transferred to .i as it showed: /lib/cpp -DSTRESS -DMPI -P -D'POINTER=integer' -I/usr/local/encap/mpich-125-2-intel/include/filename.f > filename.i cp filename.i filename.tmp.f mv filename.tmp.o filename.o rm filename.i for some of the file, after the .f changed to tmp.f, some of the statements are moved to the left, so the format of the file is messed up, for eg. 100 close changed to 100 close does any one have similiar experience? anyone have any suggestions? thank you! best wishes, R.Z ********************************************************************** Ms Ru-Zhen Li 0044-020-78826327 r.li!at!qmul.ac.uk http://www.freewebs.com/lrz/ Materials Department Queen Mary University of London E1 4NS ********************************************************************** From chemistry-request@ccl.net Thu Jan 13 15:14:28 2005 Received: from davapc1.bioch.dundee.ac.uk (davapc1.bioch.dundee.ac.uk [134.36.65.39]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0DKEQqd022724 for ; Thu, 13 Jan 2005 15:14:27 -0500 Received: from davapc1.bioch.dundee.ac.uk (localhost [127.0.0.1]) by davapc1.bioch.dundee.ac.uk (8.12.10/8.12.10) with ESMTP id j0DKEFEK011866; Thu, 13 Jan 2005 20:14:15 GMT Received: from localhost (vdava@localhost) by davapc1.bioch.dundee.ac.uk (8.12.10/8.12.10/Submit) with ESMTP id j0DKEAFR011863; Thu, 13 Jan 2005 20:14:10 GMT Date: Thu, 13 Jan 2005 20:14:10 +0000 (GMT) From: Daan van Aalten To: Luca Fenu cc: chemistry!at!ccl.net Subject: Re: CCL:assigning protonation states In-Reply-To: <41E6413F.1000106!at!soton.ac.uk> Message-ID: References: <41E6413F.1000106!at!soton.ac.uk> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII 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 PRODRG http://davapc1.bioch.dundee.ac.uk/prodrg does this Daan On Thu, 13 Jan 2005, Luca Fenu wrote: > Dear CClers > > I'm looking for some program able to automatically (and reliably) assign > protonation states at Phisiological pH to small organic molecules, > preferably saved as mol2 files. As I can expect my boss ranting if he's > to shed any money for it, any freeware alternative would be more than > welcome. Any suggestion? many thanks > > luca > -- > Real programmers don't comment! > It was hard to write, It should be hard to read! > > > > -= 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 Jan 13 20:59:39 2005 Received: from out-mail03.yourhostingaccount.com (mailrelay4.yourhostingaccount.com [38.113.1.63]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0E1xcDe005999 for ; Thu, 13 Jan 2005 20:59:38 -0500 Message-Id: <200501140159.j0E1xcDe005999..at..server.ccl.net> Received: from scan08.yourhostingaccount.com ([10.1.1.238] helo=scan08.yourhostingaccount.com) by mail03.yourhostingaccount.com with esmtp (Exim) id 1CpGkU-0007kJ-2n for chemistry..at..ccl.net; Thu, 13 Jan 2005 20:59:38 -0500 Received: from ant.yourhostingaccount.com ([10.1.1.203] ident=exim) by scan08.yourhostingaccount.com with spamscanlookuphost (Exim) id 1CpGkT-0001Ms-0M for chemistry..at..ccl.net; Thu, 13 Jan 2005 20:59:38 -0500 Received: from ant.yourhostingaccount.com ([10.1.1.203] helo=smtp.yourhostingaccount.com) by scan08.yourhostingaccount.com with esmtp (Exim) id 1CpGkS-0001Mh-Og for chemistry..at..ccl.net; Thu, 13 Jan 2005 20:59:36 -0500 Received: from adsl-64-166-142-98.dsl.snfc21.pacbell.net ([64.166.142.98] helo=Hummer) by smtp.yourhostingaccount.com with asmtp (Exim 4.34) id 1CpGkR-0004Md-VJ ; Thu, 13 Jan 2005 20:59:36 -0500 From: "Warren DeLano" To: Subject: Stereo-3D in a Window: Not in MacOS X Tiger?!! Date: Thu, 13 Jan 2005 17:58:50 -0800 MIME-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: Microsoft Office Outlook, Build 11.0.5510 In-Reply-To: <20050113013021.4C1DE4CC5A90..at..lists.apple.com> X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 Thread-Index: AcT5D3SktBdOnZsVS2uzJD56dd0bgQAj4lBA X-UserInfo: dfab58b57aa3bb910bf055c23b06c5c7:c10f421fef69a2b5fe207cfa50def74f X-User: warren_1 Sender: "Warren DeLano" X-Spam-Status: No, hits=1.1 required=7.5 tests=MY_DSL,PLING_QUERY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Fellow Visualization Software Users: My #1 gripe with MacOS X Panther has been the lack of support for industry-standard stereo-3D graphics (in a window). So far, I and others have been unable to convince Apple that this feature matters enough to their bottom line to merit implementation. Candid discussions this week at MacWorld confirmed that Tiger (OS X 10.4) will likewise ship without this essential capability at a time when the opportunity for Apple is at its peak in this market. I believe this would be a serious error, and that Apple must now hear from us on this issue. If you agree, then please reply directly to me, RIGHT NOW (mailto:warren..at..delsci.com) with the words: "Stereo 3D matters to me." Your response will be printed, and I will hand-deliver them to Apple management in nearby Cupertino at the end of the month. We need AS MANY responses as we can get (ideally 1,000+), so please forward this email to all of your visualization-oriented colleagues (in any sector), and ask them to submit individual emails to me as well. Here's why: Stereoscopic 3D visualization increasingly matters in science, medicine, and engineering. Though arguably the ultimate technical computing platform, the Mac remains hopelessly crippled in this key respect when compared to Sun, HP, Dell, or IBM workstations running Linux, Solaris, or even Windows. Dual-Xeon and dual-Opteron systems now ship stereo-3D-ready thanks to powerful nVidia/Quadro and ATI/FireGL graphics cards. Thus, the competition WILL OWN THIS MARKET if Apple doesn't support stereo-3D in a window on MacOS X, ASAP. The disruptive market opportunity created by the implosion of SGI and the stopgap adoption of "home brew" Linux systems is about to end. Professional-grade stereoscopic visualization is now a standard OpenGL capability, it is vendor-supported on a variety of hardware, and it is present on every platform EXCEPT THE MAC. None of those "amazing features" in Tiger matter one bit to technical users whose basic needs remain unmet. Stereo-3D inadequacy is a show-stopper for many scientists and engineers. The Mac will not have a fair shot at this market unless Apple quickly follows though on it's assumed responsibility to support all OpenGL features, including quad-buffered stereo-3D graphics in a window. Case in point: my company just spent $5k on a dual-Opteron Sun workstation instead of a dual-G5 Mac solely because stereo-3D in a window is absent from MacOS X. This pattern will surely be amplified many thousand-fold if Apple does not take immediate corrective action. Responding together, we can insure that Apple understands what this deficiency means for the future of MacOS X in scientific, medical, and technical visualization. I do not believe that Apple management has made an informed decision regarding stereo-3D, and I think this is our last best chance to change things before the issue becomes moot. Please share your concerns by responding to this email (mailto:warren..at..delsci.com). It will only take a second, but the benefits could last for years to come if Apple listens well and then acts decisively. Input from current Linux and Windows users is especially welcome, since Apple would love to sell you the visualization platform of your dreams if you're willing to help define it. Thank you for your time. Cheers, Warren Author of PyMOL: http://pymol.sf.net (Note that MacPyMOL is currently shown on http://apple.com/science under "The Tools" -- cool!) DeLano Scientific LLC company profile: http://delanoscientific.com/about.html PS. An alternate way to be heard is to post on the Apple SciTech or Sci-Vis mailing lists, but please CC me too to be sure that you're counted. http://lists.apple.com/mailman/listinfo/scitech http://lists.apple.com/mailman/listinfo/sci-vis -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:warren..at..delsci.com From chemistry-request@ccl.net Fri Jan 14 08:38:51 2005 Received: from fe08.axelero.hu (fe08.axelero.hu [195.228.240.96]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0EDcnII007840 for >ccl.net>; Fri, 14 Jan 2005 08:38:50 -0500 Received: from fe08 (localhost-02 [127.0.2.1]) by fe08.axelero.hu (8.12.11/8.12.11) with SMTP id j0EDcmMh021513 for >ccl.net>; Fri, 14 Jan 2005 14:38:48 +0100 (CET) Received: from fe08.axelero.hu [127.0.2.1] via SMTP gateway by fe08 [195.228.240.96]; id A053F67932F at Fri, 14 Jan 2005 14:38:48 +0100 Received: from [127.0.0.1] (18.76-182-adsl-pool.axelero.hu [81.182.76.18]) (authenticated bits=0) by fe08.axelero.hu (8.12.11/8.12.11) with ESMTP id j0EDcdhT021220 for >ccl.net>; Fri, 14 Jan 2005 14:38:47 +0100 (CET) Message-ID: <41E7CA8A.7080209<>chemaxon.hu> Date: Fri, 14 Jan 2005 14:35:06 +0100 From: Szabolcs Csepregi >chemaxon.hu> User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry<>ccl.net Subject: CCL:assigning protonation states References: <41E6413F.1000106<>soton.ac.uk> In-Reply-To: <41E6413F.1000106<>soton.ac.uk> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=3.5 required=7.5 tests=MY_DSL,RCVD_IN_DYNABLOCK, RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear Luca, Marvin has relevant calculator plugins for related tasks, namely the "major microspecies" and "pKa" plugins. "Major microspecies" is able to generate the highest concentration protonation state at a given pH, and "pKa" can show the distributions of each microspecies concentration along the whole pH range. Marvin plugins are accessible from the Marvin GUIitself, but you can use them in JAVA programs using these classes: http://www.chemaxon.com/marvin/doc/api/chemaxon/marvin/calculations/MajorMicrospeciesPlugin.html http://www.chemaxon.com/marvin/doc/api/chemaxon/marvin/calculations/pKaPlugin.html (there is some example code in the class headers) Furthermore, we provide the command line tool cxcalc: cxcalc majorms -H 3.2 test.mol id major-ms 1 [NH3+]C1C(Cl)OC(C(CCl)C1C([O-])=O)C([O-])=O (You set the pH in -H) In the following release there will be possible to set the major-ms format other than SMILES (e.g. mol or sdf) but sorry, no mol2 support in marvin. I suggest to use something like Open Babel for converting the results. For a list of command line parameters, type: cxcalc majorms -h And finally about the price tag: From your email address it seems that you are in academia, so you can join the ChemAxon academic program and use any of our software free of charge. For more information about this and to download marvin, please visit www.chemaxon.com Best regards, Szabolcs --- Szabolcs Csepregi, PhD ChemAxon Ltd., Maramaros koz 3/A, Budapest, 1037 Hungary http://www.chemaxon.com Tel: +361 4532661 From chemistry-request@ccl.net Thu Jan 13 11:58:01 2005 Received: from mail2.qmul.ac.uk (mail2.qmul.ac.uk [138.37.6.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j0DGw0qd012096 for ; Thu, 13 Jan 2005 11:58:00 -0500 Received: from smtp.qmul.ac.uk ([138.37.6.40]) by mail2.qmul.ac.uk with esmtp (Exim 4.43) id 1Cp8II-0001nY-2T for chemistry*at*ccl.net; Thu, 13 Jan 2005 16:57:58 +0000 Received: from ruzhen.mats.qmul.ac.uk ([138.37.43.64] helo=Ruzhen) by smtp.qmul.ac.uk with smtp (Exim 4.34) id 1Cp8IH-0002sS-Uw for chemistry*at*ccl.net; Thu, 13 Jan 2005 16:57:57 +0000 Message-ID: <002e01c4f990$8479d400$402b258a@Ruzhen> From: "Ru-Zhen Li" To: References: <20041209174625.55625.qmail*at*web50410.mail.yahoo.com> <200501130906.00816.alessandro.contini*at*unimi.it> Subject: Re: CCL:IRC with G03 Date: Thu, 13 Jan 2005 16:54:16 -0000 MIME-Version: 1.0 Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2900.2180 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 X-Sender-Host-Address: 138.37.43.64 X-QM-Scan-Virus: virusscan says the message is clean X-QM-Scan-Virus: ClamAV says the message is clean X-Spam-Status: No, hits=5.0 required=7.5 tests=NO_RDNS2,WLS_URI_OPT_76 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear all, I am compiling some software with MPI, and the command is: $(MAKE) LD="ifort -o" \ LDFLAGS="-L/usr/local/encap/mpich-125-2-intel/lib -lmpich -lpmpich" \ FC=ifort FFLAGS="-c -O -B100" TIMER="" \ CPFLAGS="-D$(STRESS) -DMPI -P -D'POINTER=integer' \ -I/usr/local/encap/mpich-125-2-intel/include/" \ EX=$(EX) BINROOT=$(BINROOT) $(TYPE) during the compilation, the source file .f are transferred to .i as it showed: /lib/cpp -DSTRESS -DMPI -P -D'POINTER=integer' -I/usr/local/encap/mpich-125-2-intel/include/filename.f > filename.i cp filename.i filename.tmp.f mv filename.tmp.o filename.o rm filename.i for some of the file, after the .f changed to tmp.f, some of the statements are moved to the left, so the format of the file is messed up, for eg. 100 close changed to 100 close does any one have similiar experience? anyone have any suggestions? thank you! best wishes, R.Z ********************************************************************** Ms Ru-Zhen Li 0044-020-78826327 r.li*at*qmul.ac.uk http://www.freewebs.com/lrz/ Materials Department Queen Mary University of London E1 4NS **********************************************************************