From chemistry-request@server.ccl.net Mon Aug 13 02:38:49 2001 Received: from mail.kemi.dtu.dk ([130.225.67.150]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7D6cmv08775 for ; Mon, 13 Aug 2001 02:38:49 -0400 Received: from [192.38.70.75] (pon.ok.dtu.dk [192.38.70.75]) by mail.kemi.dtu.dk (8.11.4/8.11.4) with ESMTP id f7D6Xl511092; Mon, 13 Aug 2001 08:33:48 +0200 Mime-Version: 1.0 X-Sender: pon@mail.kemi.dtu.dk Message-Id: In-Reply-To: References: Date: Mon, 13 Aug 2001 08:33:03 +0200 To: Alexander Kulak From: Per-Ola Norrby Subject: Re: CCL:1,5-Diaminotetrazole aminogroup structure Cc: chemistry@ccl.net Content-Type: text/plain; charset="us-ascii" ; format="flowed" Hi, Alexander Kulak wrote: > "N6" ------> NH2 > | > // \ > N N - NH2 <------ "N5" > | | > N = N > >X-ray investigation of this compound shows that N6 aminogroup >is planar (angles = 118,118,119) and lies in the tetrazole plane. > >But MP2/6-31G(d,p) calculation gives the non-planar structure of that >aminogroup (112,113,114 degrees), although H atoms lie close to the >ring plane, >in contrast with N5, where they lie at the different sides of the plane. > >The HOMO is combined from p(z)-AO of ring's nitrogens and p(z) of N6, >confirming common assumpion about Pi-conjugation of ring and N6. >At the same time localization (Boys or Pipek-Mezey) gives a clear >picture of lone-pair at N6. > >Could anyone please answer the QUESTIONS: > >1) Why calculated N6 is not planar while nature says it is planar? >2) Why it CAN be planar? First of all, MP2 is not the final computational answer, and also very important, X-ray is not the final answer about nature. It is quite common to find that "planar" X-ray structures are in fact pyramidal when investigated in gas phase (amides are good examples of this). In your case, planarity will be favored by crystal packing, and by hydrogen bonding which increases the conjugation. Ways to address this computationally would include investigating the planar form (lock it in Cs symmetry, compare the energy and vibrations to the planar form), or to add hydrogen bonds (preferably you should calculate the crystal with periodic boundaries; no, I don't have a program for that, but I believe there are solid-state DFT programs that can do it). One more point: The X-ray does not show you the position of the hydrogen nuclei, but if it is a very good quality X-ray, you may see the maximum density of the electrons forming the N-H bond. It is well known that this point does NOT coincide with the position of the hydrogen nucleus. Hydrogen positions are always systematically "wrong" by 0.1-0.2 A in any high-quality X-ray structure. Best regards, Per-Ola Norrby -- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Per-Ola Norrby, Assoc. Professor, http://compchem.dfh.dk/PeO/ Technical University of Denmark, Dept. of Chem., Org. Chem. Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark Email: pon@kemi.dtu.dk tel +45-45252123, fax +45-45933968 From chemistry-request@server.ccl.net Mon Aug 13 08:06:02 2001 Received: from hkusua.hku.hk ([147.8.2.91]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7DC61v29795 for ; Mon, 13 Aug 2001 08:06:01 -0400 Received: from win95pc ([147.8.148.66]) by hkusua.hku.hk (8.11.4/8.11.4) with SMTP id f7DC6vH10942 for ; Mon, 13 Aug 2001 20:06:57 +0800 (HKT) Message-ID: <004f01c123f0$76509400$42940893@win95pc.hku.hk> From: "dwang" To: Subject: summary: problem on memory. Date: Mon, 13 Aug 2001 20:07:02 +0800 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_004C_01C12433.842788C0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 This is a multi-part message in MIME format. ------=_NextPart_000_004C_01C12433.842788C0 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: quoted-printable Hi all, Some days ago I posted a problem about the distribution of memory and = some warm-hearted cclers gave me some helpful advice. Many thanks to = Mikael J., Dirk Dettmering, Peter Burger, Fredrick C. Hagemeister, Jim = Kress. Following is the summary of my former question and all of the = replies. *****************my question******************* I just bought a pc with p4 1.7G, 1G memory, asus mainboard(in the manual = it can support memory up to 2G). OS is windows98. When i run Gaussian98, = I can't set the memory distributed to G98 more than 250MB, and if I = start the Norton Antivirous real-time scan, i can't run ms-dos because = of low memory(information on the computer) but I think that no more than = 500MB memory is used at the time. Where is the rest memory? If i remove = 500MB memory, everything goes ok except that I still can't set the = memory to G98 more than 250MB. Why??? Is it because of G98 or Win98? Any = advices will be appreciated. ***************************Mikael J.*************** Windows 95/98/ME can not properly handle systems with more memory than = 512MB. See = http://support.microsoft.com/support/kb/articles/Q253/9/12.ASP You need = Linux or Windows 2000. ********************Dirk Dettmering*************** It,s caused by your OS. You have an OS for Gaming not for Gamess (sorry = for the comparison, but I couldn't resist)! Win95/98/Me can't use more = than 512 MB but do get even slower above 256 MB (the reason for this ist = the cache sizes). Get a serious OS, preferably linux, but Windows NT can also cope with = this amount of memory. ********************Peter Burger**************************** Problem is Win9x does not support more than 800 MB max. - it is a = problem with the vcache device driver this number includes the AGP = aperture size though. - better get a license of WIN2K or NT4 their = memory management is superior anyways. check = http://support.microsoft.com knowledge base Q253912 *****************Gregory Shamov*************************** AFAIK its because of Win98. Try Win2000. There are much more reasons to = use Windows NT family instead of Win9x than 256MB memory limit in the = latter. In fact, no one researcher I know is using Win9x for production = calculations, because of its buggy and unstable nature. **********************Fredrick C. Hagemeister************************* The switch to Windows 2000 would also be good for speed and stability. = There is a significant time savings going between G98W to Win2K. Also, = I think everyone will testify that Win2K crashes less than Win98. On = the other hand, I found a great free front end for Gaussian called WebMO = (www.webmo.net) that requires Linux on the G98 machine. It is a server-based, web application. The user interfaces with the server with = any web browser anywhere and can visually construct, submit, and see the = output from the jobs. *********************Jim Kress***************************** That's not really true. If you read the article you'll see that 98/ME = will work with > 512MB RAM, all you have to do is : "Use the MaxFileCache setting in the System.ini file to reduce the = maximum amount of memory that Vcache uses to 512 megabytes (524,288 KB) = or less. " I routinely run 768 MB of RAM under Windows ME using applications like = pcGAMESS and have no problem getting all the memory I need. Wang Dongqi ------=_NextPart_000_004C_01C12433.842788C0 Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: quoted-printable
Hi = all,
 
Some = days ago I posted a problem about=20 the distribution of memory and some warm-hearted cclers gave me some = helpful=20 advice. Many thanks to Mikael J., Dirk Dettmering, Peter Burger, = Fredrick C.=20 Hagemeister, Jim Kress. Following is the summary of my former question = and all=20 of the replies.
 
*****************my=20 question*******************
I just bought a pc with p4 1.7G, 1G memory, asus mainboard(in = the manual=20 it can support memory up to 2G). OS is windows98. When i run Gaussian98, = I can't=20 set the memory distributed to G98 more than 250MB, and if I start the = Norton=20 Antivirous real-time scan, i can't run ms-dos because of low = memory(information=20 on the computer) but I think that no more than 500MB memory is used at = the time.=20 Where is the rest memory? If i remove 500MB memory, everything goes ok = except=20 that I still can't set the memory to G98 more than 250MB. Why??? Is it = because=20 of G98 or Win98? Any advices will be appreciated.
***************************Mikael=20 J.***************
Windows 95/98/ME can not properly=20 handle systems with more memory than 512MB. See h= ttp://support.microsoft.com/support/kb/articles/Q253/9/12.ASP=20 You need Linux or Windows 2000.
 
********************Dirk=20 Dettmering***************
It,s = caused by your OS. You have an OS=20 for Gaming not for Gamess (sorry for the comparison, but I couldn't = resist)!=20 Win95/98/Me can't use more than 512 MB but do get even slower above 256 = MB (the=20 reason for this ist the cache sizes).
Get a serious OS, preferably = linux, but=20 Windows NT can also cope with this amount of memory.

 
********************Peter=20 Burger****************************
Problem is Win9x does not=20 support more than 800 MB max. - it is a problem with the vcache device = driver=20 this number includes the AGP aperture size though.  - better get a = license=20 of WIN2K or NT4 their memory management is  superior anyways. check = http://support.microsoft.com = knowledge=20 base Q253912

*****************Gregory=20 Shamov***************************
AFAIK its because of Win98. Try Win2000. There are much more = reasons to use=20 Windows NT family instead of Win9x than 256MB memory limit in the = latter. In=20 fact, no one researcher I know is using Win9x for production = calculations,=20 because of its buggy and unstable nature.

**********************Fredrick C.=20 Hagemeister*************************
The switch to Windows 2000 would also be good for speed and = stability.=20 There is a significant time savings going between G98W to Win2K.  = Also, I=20 think everyone will testify that Win2K crashes less than Win98.  On = the=20 other hand, I found a great free front end for Gaussian called WebMO (www.webmo.net) that requires Linux on = the G98=20 machine.  It is a
server-based, web application.  The user=20 interfaces with the server with any web browser anywhere and can = visually=20 construct, submit, and see the output from the jobs.
 
*********************Jim Kress*****************************
That's not really true.  If you read the article you'll see = that 98/ME=20 will work with > 512MB RAM, all you have to do is :

"Use = the=20 MaxFileCache setting in the System.ini file to reduce the maximum amount = of=20 memory that Vcache uses to 512 megabytes (524,288 KB) or less. = "

I=20 routinely run 768 MB of RAM under Windows ME using applications like = pcGAMESS=20 and have no problem getting all the memory I need.
 
Wang Dongqi
------=_NextPart_000_004C_01C12433.842788C0-- From chemistry-request@server.ccl.net Mon Aug 13 13:24:59 2001 Received: from uranium.camsoft.com ([198.112.109.92]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7DHOxv04137 for ; Mon, 13 Aug 2001 13:24:59 -0400 Received: from [198.112.110.146] (198.112.110.146) by uranium.camsoft.com (Worldmail 1.3.167) for chemistry@ccl.net; 13 Aug 2001 13:24:59 -0400 Message-ID: <3B66A849000016DD@uranium.camsoft.com> (added by uranium.camsoft.com) Date: 13 Aug 01 13:23:16 -0400 From: Kam Chana Subject: CambridgeSoft Chem3D Plugin and Microsoft IE compatibility To: chemistry X-Mailer: QuickMail Pro 1.5.2 (Mac) X-Priority: 3 MIME-Version: 1.0 Reply-To: Kam Chana Content-Type: text/plain; charset="US-Ascii" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f7DHOxv04138 August 13, 2001 Microsoft has recently released Service Pack 2 for Microsoft Internet Explorer (5.5 SP2) which does not support the Netscape plugin architecture. According to Microsoft future releases of Internet Explorer will also not support the plugin architecture. CambridgeSoft is pleased to announce that its Chem3D browser plugin will not be affected by this change. The latest Chem3D plugin, v6.0.1, which is now available from our support site, can be deployed immediately to view web pages that contain 3D molecular models. It supports all the common data formats including MDL MOL files and Brookhaven PDB formats. A compatible version of the ChemDraw plugin will be available soon. Further information and the plugin installer are available at the following site: http://www.cambridgesoft.com/support/ Click on Downloads to view the Downloads page Select Chem3D in Product and choose the Windows platform on the Downloads page Submit request and download the ChemOffice Net Plugin 6.0.1 CambridgeSoft Corp. www.cambridgesoft.com From chemistry-request@server.ccl.net Mon Aug 13 15:02:13 2001 Received: from cascara.uvic.ca (root@[142.104.5.28]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7DJ2Dv06002 for ; Mon, 13 Aug 2001 15:02:13 -0400 Received: from unix5.uvic.ca (unix5.uvic.ca [142.104.5.117]) by cascara.uvic.ca (8.11.3/8.11.3) with ESMTP id f7DJ2C1151924; Mon, 13 Aug 2001 12:02:12 -0700 Date: Mon, 13 Aug 2001 12:02:12 -0700 (PDT) From: Roy Jensen To: cc: Subject: Re: CCL:summary: problem on memory. In-Reply-To: <004f01c123f0$76509400$42940893@win95pc.hku.hk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII A second question was asked as well, namely that G98W doesn't accept more than 250MB in the default.route file. I also have hit this limitation and assumed it to be due to G98W, akin to the single-processor and 2 GB scratch file limitations. (A detailed discussion is available in the CCL archives.) Roy Jensen From chemistry-request@server.ccl.net Mon Aug 13 16:49:13 2001 Received: from oco.net ([216.171.163.254]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7DKnCv08141 for ; Mon, 13 Aug 2001 16:49:12 -0400 Received: from Hppav [64.20.154.53] by oco.net (SMTPD32-6.06) id AD3CEF0120; Mon, 13 Aug 2001 13:49:00 -0700 Message-ID: <001f01c12439$6136c640$0100a8c0@oco.net> From: "Jim Kress" To: References: Subject: Re: CCL:summary: problem on memory. Date: Mon, 13 Aug 2001 16:48:59 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 I don't think250MB limit is correct. I have routinely used 960MB for G98W calculations in Windows NT. You might be right if you said 250MW (i.e. mega words). That would be 2GB which is the limit for a 32bit addressing system like Windows. Jim ----- Original Message ----- From: "Roy Jensen" To: Cc: Sent: Monday, August 13, 2001 3:02 PM Subject: CCL:summary: problem on memory. > A second question was asked as well, namely that G98W doesn't accept more > than 250MB in the default.route file. I also have hit this limitation and > assumed it to be due to G98W, akin to the single-processor and 2 GB > scratch file limitations. (A detailed discussion is available in the CCL > archives.) > > Roy Jensen > > > > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > From chemistry-request@server.ccl.net Mon Aug 13 11:00:17 2001 Received: from mercure.IRO.UMontreal.CA (IDENT:root@[132.204.24.67]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7DF0Hv01921; Mon, 13 Aug 2001 11:00:17 -0400 Received: from orage.IRO.UMontreal.CA (IDENT:root@orage.IRO.UMontreal.CA [132.204.26.240]) by mercure.IRO.UMontreal.CA (8.11.4/8.11.1) with ESMTP id f7DF0HB02291; Mon, 13 Aug 2001 11:00:17 -0400 Received: from localhost (levacf@localhost) by orage.IRO.UMontreal.CA (8.11.4/8.11.1) with ESMTP id f7DF0GE16699; Mon, 13 Aug 2001 11:00:16 -0400 Date: Mon, 13 Aug 2001 11:00:16 -0400 (EDT) From: Francois Levac To: chemistry@ccl.net cc: mailserv@ccl.net Subject: PDB structure of aminoglycosides Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id f7DF0Hw01922 Hello, I don't know if I am at the right place, but I am searching a structure of aminoglycosides with the hydrogens included. I already have a PDB file of paromomycine but the hydrogens are lacking. I would prefer to have these structure in PDB format but other formats are also good. I would like to have structure of these aminoglycosides: paromomycin, neomycin B, tobramycin, kanamycin, streptomycin and gentamycin. Thank you very much for your help. François Levac M.Sc. student Bio-informatics University of Montreal levacf@iro.umontreal.ca From chemistry-request@server.ccl.net Mon Aug 13 08:29:55 2001 Received: from mail.etang.com ([202.101.42.207]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7DCTsv30431 for ; Mon, 13 Aug 2001 08:29:55 -0400 Received: from lizhenhua (unknown [202.108.240.3]) by mail.etang.com (Postfix) with ESMTP id 0F59A1C996BCB for ; Mon, 13 Aug 2001 20:37:59 +0800 (CST) Message-ID: <006e01c123f3$eace53a0$c40b140a@lizhenhua> From: "Zhenhua Li" To: "CCL" Subject: g98 error on linux Date: Mon, 13 Aug 2001 20:31:45 +0800 Organization: Chem. Dept. Fudan Univ. Shanghai, China MIME-Version: 1.0 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2479.0006 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2479.0006 Dear CCLers, When I ran g98 in Linux Redhat 7.1. But following error appeared: g98: error while loading shared libraries: /home/scratch/test/g98/util.so: undefined symbol: fstat Nothing appeared in output file at all. I can't find out what's wrong with it. Can anyone help me? Thanks in advance. Li Zhenhua From chemistry-request@server.ccl.net Mon Aug 13 17:20:38 2001 Received: from web13406.mail.yahoo.com ([216.136.175.64]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f7DLKcv08824 for ; Mon, 13 Aug 2001 17:20:38 -0400 Message-ID: <20010813212037.37363.qmail@web13406.mail.yahoo.com> Received: from [169.232.140.206] by web13406.mail.yahoo.com; Mon, 13 Aug 2001 14:20:37 PDT Date: Mon, 13 Aug 2001 14:20:37 -0700 (PDT) From: eric hu Subject: experimental solvation data in acetonitrile To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi, I wonder if anyone knows the liturature of common molecules solvation in CH3CN. Thanks! Eric __________________________________________________ Do You Yahoo!? Send instant messages & get email alerts with Yahoo! Messenger. http://im.yahoo.com/