From chemistry-request@server.ccl.net Tue Feb 5 06:19:46 2002 Received: from sagres.tcc (user@[193.137.208.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g15BJjc06223 for ; Tue, 5 Feb 2002 06:19:46 -0500 Received: from ci.uc.pt (localhost.localdomain [127.0.0.1]) by sagres.tcc (8.11.6/8.11.6) with ESMTP id g15BOdi10449 for ; Tue, 5 Feb 2002 11:24:43 GMT Sender: jorge@sagres.tcc Message-ID: <3C5FC0F7.42FC23AF@ci.uc.pt> Date: Tue, 05 Feb 2002 11:24:39 +0000 From: Jorge Manuel Campos Marques X-Mailer: Mozilla 4.78 [en] (X11; U; Linux 2.4.9-7 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Complex matrix diagonalization routine Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear cclers, We need a complex matrix diagonalization routine in fortran 77. We have already tried one from EISPACK called CG.F, but it does not work very well. Could you kindly tell me another one? Thanking in advance J. Marques From chemistry-request@server.ccl.net Mon Feb 4 17:56:27 2002 Received: from alien.biochem.wfubmc.edu ([152.11.118.46]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g14MuRc19224 for ; Mon, 4 Feb 2002 17:56:27 -0500 Received: from localhost (zhangxd@localhost) by alien.biochem.wfubmc.edu (8.11.6/8.11.6) with ESMTP id g14MuHT1350157; Mon, 4 Feb 2002 17:56:17 -0500 (EST) Date: Mon, 4 Feb 2002 17:56:17 -0500 From: Zhangxd To: Jeff Nauss cc: chemistry@ccl.net Subject: how i can get detailed secondary structure from coordinate file? In-Reply-To: <5.1.0.14.0.20020204090052.01f82048@sparky2.sd.accelrys.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, during my research, i need the detailed information about secondary structure of my biology system, i had its coordinate file, how i can get its secondary structure information from this coordinate file? just like the following: Resi. 1 to Resi. 10 AlphaHelix Resi. 15 to Resi. 25 BetaSheet .................. ............... hopefully it should be a program can do this automatically. i had tried VMD, it just gives the graph of secondary structure of the sequence but not a detailed text information like the above sample. thanks in advance!!!! From chemistry-request@server.ccl.net Tue Feb 5 12:28:10 2002 Received: from red.CACheSoftware.com (IDENT:root@[12.17.172.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g15HS9c12768 for ; Tue, 5 Feb 2002 12:28:09 -0500 Received: from daveg.cachesoftware.com ([192.168.110.100]) by red.CACheSoftware.com (8.11.6/8.9.3/3) with ESMTP id g15Hc2413494; Tue, 5 Feb 2002 09:38:02 -0800 Message-Id: <5.1.0.14.0.20020205083037.03466720@pop3.norton.antivirus> X-Sender: daveg/mail.cachesoftware.com@pop3.norton.antivirus X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Tue, 05 Feb 2002 09:27:21 -0800 To: Zhangxd From: David Gallagher Subject: Re: CCL:how i can get detailed secondary structure from coordinate file? Cc: chemistry@ccl.net In-Reply-To: References: <5.1.0.14.0.20020204090052.01f82048@sparky2.sd.accelrys.com> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Secondary structure: BioMedCAChe can import a pdb file and display the 3-D structure in one window and the full sequence with the secondary structure in a second window. The secondary structure is from the pdb assignment or computed by the Kabsch & Sander method. The sequence is labeled by residue number, name and secondary structure. You can select, insert, delete, edit, etc. in either of the interactive windows. I am not sure if this helps, but you can get a fully functional evaluation copy for Windows from www.cachesoftware.com to test. David Gallagher, Fujitsu At 05:56 PM 2/4/2002 -0500, Zhangxd wrote: >Dear All, >during my research, i need the detailed information about secondary >structure of my biology system, i had its coordinate file, how i can get >its secondary structure information from this coordinate file? just like >the following: >Resi. 1 to Resi. 10 AlphaHelix >Resi. 15 to Resi. 25 BetaSheet > >.................. > >............... > >hopefully it should be a program can do this automatically. >i had tried VMD, it just gives the graph of secondary structure of >the sequence but not a detailed text information like the above sample. > >thanks in advance!!!! > > > >-= 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 Tue Feb 5 13:42:13 2002 Received: from lgdx04.lg.ehu.es ([158.227.1.36]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g15IgCc15807 for ; Tue, 5 Feb 2002 13:42:13 -0500 Received: by lgdx04.lg.ehu.es id TAA0000010602; Tue, 5 Feb 2002 19:42:02 +0100 (MET) Message-ID: <007001c1ae74$840a6e40$222fe39e@lc.ehu.es> From: "Pablo Vitoria" To: "CCL" Subject: =?iso-8859-1?Q?=BFWhat_do_you_think_of_this_computer=3F?= Date: Tue, 5 Feb 2002 19:39:59 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_006D_01C1AE7C.E5B4E5A0" 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 This is a multi-part message in MIME format. ------=_NextPart_000_006D_01C1AE7C.E5B4E5A0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi all, I am sorry to bother you all with this kind of "best computer" question. = But I will try to be very specific: - I want to run mainly G98, but also GAMESS (and probably ADF) on a dual = Linux machine. - My calculations are of the DFT type on big molecules with several = transition metals each. - I don't feel prepared to build and maintain a cluster, so I'd rather = buy a top-range dual box. - I have been offered the following computer (it costs as much as I can = expend...about 5000 euro), which seems OK to me, but I don't want to = waste money: Supermicro P4DC6+ Motherboard with 400MHz bus 2 x Intel Xeon 2GHz 512 Cache 4 x 256MB RIMM RAM Seagate Cheetah 18,2Gb UltraSCSI 160 10000rpm Hard Disk CD Rom, keyboard,...... My question is: =BFcan I get the same power at a lower cost? I mean: Is = the RIMM or UltraSCSI hard disk really necessary? Will this computer = outperform a dual Athlon with a 133MHz bus, which I know is MUCH = cheaper? Thank you very much for all your help Pablo -------------------------------------------------------- Pablo Vitoria Garcia Dpto. Qu=EDmica Inorg=E1nica, Facultad de Ciencias Universidad del Pa=EDs Vasco (UPV/EHU) Aptdo. 644 48080 Bilbao (Bizkaia) Tfno. 94 6012579 Fax. 94 4648500 ------=_NextPart_000_006D_01C1AE7C.E5B4E5A0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi all,
 
I am sorry to bother you all with this = kind of=20 "best computer" question. But I will try to be very = specific:
 
- I want to run mainly G98, but also=20 GAMESS (and probably ADF) on a dual Linux machine.
- My calculations are of the DFT type = on big=20 molecules with several transition metals each.
- I don't feel prepared to build and = maintain a=20 cluster, so I'd rather buy a top-range dual box.
- I have been offered the following = computer (it=20 costs as much as I can expend...about 5000 euro), which seems OK to me, = but I=20 don't want to waste money:
 
Supermicro P4DC6+ Motherboard with = 400MHz=20 bus
2 x Intel Xeon 2GHz 512 = Cache
4 x 256MB RIMM RAM
Seagate Cheetah 18,2Gb UltraSCSI 160 = 10000rpm Hard=20 Disk
CD Rom, keyboard,......
 
My question is: =BFcan I get the same = power at a=20 lower cost? I mean: Is the RIMM or UltraSCSI hard disk really necessary? = Will=20 this computer outperform a dual Athlon with a 133MHz bus, which I know = is MUCH=20 cheaper?
 
Thank you very much for all your = help
 
Pablo
 
--------------------------------------------------------
Pabl= o Vitoria=20 Garcia
Dpto. Qu=EDmica Inorg=E1nica, Facultad de = Ciencias
Universidad del Pa=EDs=20 Vasco (UPV/EHU)
Aptdo. 644
48080 Bilbao (Bizkaia)
 
Tfno. 94 6012579
Fax. 94=20 4648500
------=_NextPart_000_006D_01C1AE7C.E5B4E5A0-- From chemistry-request@server.ccl.net Tue Feb 5 11:59:29 2002 Received: from celebris04.cetem.gov.br ([200.20.105.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g15GxSc11909 for ; Tue, 5 Feb 2002 11:59:29 -0500 Received: by correio.cetem.gov.br with Internet Mail Service (5.5.2653.19) id ; Tue, 5 Feb 2002 14:59:50 -0300 Message-ID: <34AE93248C15D611AE1600105AD16BDF056008@correio.cetem.gov.br> From: Julio Guedes To: CHEMISTRY@ccl.net Subject: Zeolites Date: Tue, 5 Feb 2002 14:59:42 -0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) 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 g15GxTc11910 Please friends, I'm wanting to Know about papers of the zeolites that using cerius or materials studio programs . Julio Cesar Guedes Correia D.Sc., Engenharia Mineral CENTRO DE TECNOLOGIA MINERAL - CETEM Ministério da Ciência e Tecnologia - MCT Coordenação de Tratamento de Minérios - CTM Serviço de Físico-Química de Superfície - SEFQ Av. Ipê, 900 - Ilha da Cidade Universitária 21941-590 - Rio de Janeiro - RJ tel.: (21) 3865-7245 fax: (21) 2560-9196 jguedes@cetem.gov.br http://www.cetem.gov.br From chemistry-request@server.ccl.net Tue Feb 5 17:48:57 2002 Received: from europium.chem.uit.no ([129.242.24.169]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g15Mmuc19997 for ; Tue, 5 Feb 2002 17:48:56 -0500 Received: from europium.chem.uit.no (localhost.localdomain [127.0.0.1]) by europium.chem.uit.no (Postfix) with ESMTP id A5BF71B02A; Tue, 5 Feb 2002 23:48:40 +0100 (CET) Date: Tue, 5 Feb 2002 23:48:40 +0100 From: Olav Fossgaard To: Pablo Vitoria Cc: chemistry@ccl.net Subject: CCL:What do you think of this computer? Message-ID: <20020205234840.A6399@europium.chem.uit.no> References: <007001c1ae74$840a6e40$222fe39e@lc.ehu.es> Mime-Version: 1.0 Content-Type: text/plain; format=flowed; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit In-Reply-To: <007001c1ae74$840a6e40$222fe39e@lc.ehu.es>; from qibvigap@lg.ehu.es on Tue, Feb 05, 2002 at 19:39:59 +0100 X-Mailer: Balsa 1.2.3 Lines: 41 On 2002.02.05 19:39 Pablo Vitoria wrote: > Hi all, > > I am sorry to bother you all with this kind of "best computer" > question. But I will try to be very specific: > Supermicro P4DC6+ Motherboard with 400MHz bus > 2 x Intel Xeon 2GHz 512 Cache > 4 x 256MB RIMM RAM > Seagate Cheetah 18,2Gb UltraSCSI 160 10000rpm Hard Disk > CD Rom, keyboard,...... > > My question is: ¿can I get the same power at a lower cost? I mean: Is > the RIMM or UltraSCSI hard disk really necessary? Will this computer > outperform a dual Athlon with a 133MHz bus, which I know is MUCH > cheaper? My two cents: Go for a dual athlon system with DDR ram and, if you can afford it, SCSI disk. You might consider a separate disk for your workspace. If SCSI is too expencive, go for an IDE RAID solution, e.g. one separate system disk and a workspace on two disks in RAID 0. Low cost IDE RAID controllers are typically about 150 euro. Our research group has recently invested in a cluster of 5 dual athlon machines with the IDE RAID solution mentioned above. When running only one I/O intensive job per node, the disk performance is roughly equal to what I get when submitting jobs to the national supercomputers. However, two I/O-intensive jobs on the same node will reduce performance drastically. For a fairly recent comparison of athlon and intel CPU's, have a look at http://www4.tomshardware.com/cpu/01q4/011031/ Best regards, Olav From chemistry-request@server.ccl.net Tue Feb 5 18:18:17 2002 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g15NIHc21390 for ; Tue, 5 Feb 2002 18:18:17 -0500 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id SAA67784; Tue, 5 Feb 2002 18:10:22 -0500 (EST) Date: Tue, 5 Feb 2002 18:10:22 -0500 From: Rick Venable To: David Gallagher cc: Zhangxd , chemistry@ccl.net Subject: Re: CCL:how i can get detailed secondary structure from coordinate file? In-Reply-To: <5.1.0.14.0.20020205083037.03466720@pop3.norton.antivirus> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII You may also wish to look at the FREE program from NLM/NCBI named "Cn3D" for protein visualization, alignment, and structural motifs. http://www.ncbi.nlm.nih.gov/PubMed/ Click on the "Structure" link and you'll find info on Cn3D It is available for M$ Windows, MacOS, and Unix. On Tue, 5 Feb 2002, David Gallagher wrote: > Secondary structure: > BioMedCAChe can import a pdb file and display the 3-D structure in > one window and the full sequence with the secondary structure in a > second window. The secondary structure is from the pdb assignment or > computed by the Kabsch & Sander method. The sequence is labeled by > residue number, name and secondary structure. You can select, > insert, delete, edit, etc. in either of the interactive windows. I > am not sure if this helps, but you can get a fully functional > evaluation copy for Windows from www.cachesoftware.com to test. > > David Gallagher, Fujitsu > At 05:56 PM 2/4/2002 -0500, Zhangxd wrote: > >Dear All, > >during my research, i need the detailed information about secondary > >structure of my biology system, i had its coordinate file, how i can get > >its secondary structure information from this coordinate file? just like > >the following: > >Resi. 1 to Resi. 10 AlphaHelix > >Resi. 15 to Resi. 25 BetaSheet > > >.................. > > >............... > > > >hopefully it should be a program can do this automatically. > >i had tried VMD, it just gives the graph of secondary structure of > >the sequence but not a detailed text information like the above sample. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@server.ccl.net Tue Feb 5 17:12:37 2002 Received: from red.CACheSoftware.com (IDENT:root@[12.17.172.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g15MCbc19172 for ; Tue, 5 Feb 2002 17:12:37 -0500 Received: from daveg.cachesoftware.com ([192.168.110.100]) by red.CACheSoftware.com (8.11.6/8.9.3/3) with ESMTP id g15MMS417872; Tue, 5 Feb 2002 14:22:28 -0800 Message-Id: <5.1.0.14.0.20020205135350.03a3e540@pop3.norton.antivirus> X-Sender: daveg/mail.cachesoftware.com@pop3.norton.antivirus X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Tue, 05 Feb 2002 14:15:58 -0800 To: chemistry@ccl.net From: David Gallagher Subject: FINAL CALL FOR PAPERS: MOPAC User Group (MUG) Meeting, Orlando ACS Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_27391657==_.ALT" --=====================_27391657==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed FINAL CALL FOR PAPERS: MOPAC User Group (MUG) Meeting, Orlando ACS You are invited to participate in the second MOPAC Users Group (MUG) Meeting, scheduled for 1pm - 4pm on Sunday April 7, 2002, at the Sheraton Hotel (Florida Bay 2) in conjunction with the Spring ACS Meeting in Orlando, FL. The MUG meeting will include submitted presentations on chemistry and biochemistry applications of MOPAC (all versions) as well as a Q&A session with the author, Dr. J. J. P. Stewart. The full itinerary will be published on the web shortly. Registration: The meeting is sponsored by Fujitsu and attendance is free, but as space is limited please register by Web: http://www.cachesoftware.com/mug/ Tel: Kim Hill at (1) 503 746 3602 Email: mailto:khill@cachesoftware.com. Presentations (20 minutes including questions): Please submit your complete contact information, title and an abstract of between 100 and 200 words to mug@cachesoftware.com by Feb 25, 2002. For more information please visit http://www.cachesoftware.com/mug/ David Gallagher --=====================_27391657==_.ALT Content-Type: text/html; charset="us-ascii"         FINAL CALL FOR PAPERS:
        MOPAC User Group (MUG) Meeting, Orlando ACS

You are invited to participate in the second MOPAC Users Group (MUG) Meeting, scheduled for 1pm - 4pm on Sunday April 7, 2002, at the Sheraton Hotel (Florida Bay 2) in conjunction with the Spring ACS Meeting in Orlando, FL. The MUG meeting will include submitted presentations on chemistry and biochemistry applications of MOPAC (all versions) as well as a Q&A session with the author, Dr. J. J. P. Stewart. The full itinerary will be published on the web shortly.

Registration: The meeting is sponsored by Fujitsu and attendance is free, but as space is limited please register by

Web: http://www.cachesoftware.com/mug/
Tel: Kim Hill at (1) 503 746 3602
Email: mailto:khill@cachesoftware.com.

Presentations (20 minutes including questions): Please submit your complete contact information, title and an abstract of between 100 and 200 words to mug@cachesoftware.com by Feb 25, 2002.

For more information please visit http://www.cachesoftware.com/mug/

David Gallagher <dgallagher@cachesoftware.com>

--=====================_27391657==_.ALT--