From chemistry-request@server.ccl.net Sat Oct 26 14:18:22 2002 Received: from medusa.wo.utoledo.edu ([131.183.69.81]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9QIIMv03663 for ; Sat, 26 Oct 2002 14:18:22 -0400 Received: from there (IDENT:w9dUksVR2eZ+Y4T7+pf70EezJ87DU2Dz@localhost.localdomain [127.0.0.1]) by medusa.wo.utoledo.edu (8.11.6/8.11.6) with SMTP id g9QIKZV08305; Sat, 26 Oct 2002 14:20:35 -0400 Message-Id: <200210261820.g9QIKZV08305@medusa.wo.utoledo.edu> Content-Type: text/plain; charset="iso-8859-1" From: Venkataraman Kabaleeswaran Reply-To: vkabale@uoft02.utoledo.edu Organization: univ of toledo To: CCL Subject: ligplot Date: Sat, 26 Oct 2002 14:20:35 -0400 X-Mailer: KMail [version 1.3.1] Cc: Iain Wallace MIME-Version: 1.0 Content-Transfer-Encoding: 8bit hi all and lain, In order to get ligplot , please send email to DR.Roman Laskowski his email is "roman@biochem.ucl.ac.uk" you can get friendly and immediate response from him. cheers venkataraman From chemistry-request@server.ccl.net Sat Oct 26 21:06:52 2002 Received: from mtiwmhc13.worldnet.att.net ([204.127.131.117]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9R16pv19227 for ; Sat, 26 Oct 2002 21:06:51 -0400 Received: from dopetec ([138.23.156.82]) by mtiwmhc13.worldnet.att.net (InterMail vM.5.01.05.xx 201-253-122-126-xxx-20020920) with ESMTP id <20021027010650.NABT12880.mtiwmhc13.worldnet.att.net@dopetec> for ; Sun, 27 Oct 2002 01:06:50 +0000 Message-ID: <013f01c27d55$21f6cdb0$529c178a@dopetec> From: "Donald Keidel" To: Subject: thermodynamic integration Date: Sat, 26 Oct 2002 18:06:50 -0700 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_013C_01C27D1A.74E9DB60" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_013C_01C27D1A.74E9DB60 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello CCLers, I am thinking of purchasing AMBER and using Gibbs to perform some = thermodynamic integration techniques. The manual, however, does not go = into too much theory regarding the TI technique used in AMBER and in = particular the equation that is actually integrated over the limits of = lambda. Does anyone know of a reference that may describe the technique = and equation in more detail. Also, does anyone know of research groups = that may have developed their own code to perform TI calculations? All = responses are appreciated. Thank you very much. -------------------------------------------------------------------------= -------------------------------------- Donald J. Keidel University of California, Riverside Department of Biochemistry and Molecular Biology Riverside, CA 92521 phone: (909) 787-5493 fax: (909) 787-4434 dkeidel397@att.net webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm ------=_NextPart_000_013C_01C27D1A.74E9DB60 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello CCLers,
 
I am thinking of purchasing AMBER and = using Gibbs=20 to perform some thermodynamic integration techniques.  The manual, = however,=20 does not go into too much theory regarding the TI technique used in = AMBER and in=20 particular the equation that is actually integrated over the limits of=20 lambda.  Does anyone know of a reference that may describe the = technique=20 and equation in more detail.  Also, does anyone know of research = groups=20 that may have developed their own code to perform TI calculations?  = All=20 responses are appreciated.  Thank you very much.
 
 
----------------------------------------------------------------= -----------------------------------------------
Donald=20 J. Keidel
University of California, Riverside
Department of = Biochemistry=20 and Molecular Biology
Riverside, CA 92521
phone:  (909)=20 787-5493
fax:  (909) 787-4434
dkeidel397@att.net
webpage: www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm<= /FONT>
 
 
------=_NextPart_000_013C_01C27D1A.74E9DB60-- From chemistry-request@server.ccl.net Sat Oct 26 13:13:46 2002 Received: from mu21.vnn.vn ([203.162.4.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9QHDiv02986 for ; Sat, 26 Oct 2002 13:13:45 -0400 Received: from chutam ([203.41.55.49]) by mu21.vnn.vn (Netscape Messaging Server 4.15) with ESMTP id H4LMIT02.9KI; Sun, 27 Oct 2002 00:13:41 +0700 From: "Truong Chu Tam" To: "'Iain Wallace'" , "'CCL'" Subject: RE: Surfnet and Ligplot and Ligbuilder Date: Sun, 27 Oct 2002 00:16:14 +0700 Message-ID: <000501c27d13$640bc9e0$313729cb@chutam> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0006_01C27D4E.106AA1E0" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2616 Importance: Normal In-Reply-To: <000a01c27c47$0b01e130$626ce286@wallaceiwork> X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 This is a multi-part message in MIME format. ------=_NextPart_000_0006_01C27D4E.106AA1E0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable You can log in to this URL by anonymous and enter your email =85. =20 =20 =20 -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net] On Behalf Of Iain Wallace Sent: Friday, October 25, 2002 11:53 PM To: CCL Subject: CCL:Surfnet and Ligplot and Ligbuilder =20 Hi all, =20 Sorry to bother you but does any one know how to get the programs ligplot and surfnet? I have tried to ftp them from ftp.biochem.ucl.ac.uk but it asks for a user name and password and I don't know how to get it. What should I do?=20 =20 I am also having trouble installing LigBuilder. I have downloaded the file but I cann't manage to decrypt it as I my e-mails keep getting bounced back when I e-mail Prof. Lai at lai@ipc.pku.edu.cn Does anyone know who I should e-mail ?=20 =20 I am a postgraduate student in TCD=20 =20 Thanks for your help again =20 Iain =20 ------=_NextPart_000_0006_01C27D4E.106AA1E0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

You can log in to this URL by = anonymous and enter your email ….

 

 

 

-----Original = Message-----
From: Computational = Chemistry List [mailto:chemistry-request@ccl.net] On Behalf Of Iain Wallace
Sent: Friday, October 25, = 2002 11:53 PM
To: CCL
Subject: CCL:Surfnet and = Ligplot and Ligbuilder

 

Hi = all,

 

Sorry to bother you but = does any one know how to get the programs ligplot and = surfnet?

how to get it. What should = I do?

 

I am also having trouble = installing LigBuilder. I have downloaded the file but I cann't manage to decrypt it = as I my e-mails keep getting

bounced back when I e-mail = Prof. Lai at lai@ipc.pku.edu.cn Does = anyone know who I should e-mail ?

 

I am a postgraduate student = in TCD

 

Thanks for your help = again

 

Iain

 

------=_NextPart_000_0006_01C27D4E.106AA1E0-- From chemistry-request@server.ccl.net Sat Oct 26 05:34:51 2002 Received: from jeeves.ccdc.cam.ac.uk ([131.111.113.44]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9Q9Yoj30455 for ; Sat, 26 Oct 2002 05:34:50 -0400 Received: from www-data by jeeves.ccdc.cam.ac.uk with local (Exim 3.35 #1 (Debian)) id 185NLD-0005Wv-00; Sat, 26 Oct 2002 10:34:47 +0100 To: Victor Ferro Subject: Re: CCL:Fwd: File convertion Message-ID: <1035624887.3dba61b789938@jeeves.ccdc.cam.ac.uk> Date: Sat, 26 Oct 2002 10:34:47 +0100 (BST) From: streek@ccdc.cam.ac.uk Cc: chemistry@ccl.net MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="-MOQ1035624887d46269b63be00190b5ce2c8050bc002c" User-Agent: IMP/PHP IMAP webmail program 2.2.6 X-Originating-IP: 80.4.1.89 This message is in MIME format. ---MOQ1035624887d46269b63be00190b5ce2c8050bc002c Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit Quoting Victor Ferro : > Dear colleagues: > I have attempted to convert the geometry contained in the attached > file > to cartesian (or internal) coordinates using Babel, but I have not > achieved to make it. > Would someone help me, please. > I will be very gratefully. > Thank you in advance > > Victor Ferro. Dear Victor, the program mentioned in the file itself can do this: # For further information visit CCDC www.ccdc.cam.ac.uk # To view the CIF, please download Mercury from this site. Mercury can be downloaded for free from http://www.ccdc.cam.ac.uk It can read your file, display it, and save it in various other formats, among them pdb and mol2 both of which contain cartesian co-ordinates. I have also converted your file into a zmatrix format, as attached. This z- matrix was generated from the centre of the molecule working outwards, so as to avoid "the tail is wagging the dog" effects, but this might not be relevant for your application. (The z-matrix was generated using a part of Mercury that is not currently publicly available.) Best wishes, -- Jacco van de Streek Research Scientist Cambridge Crystallographic Data Centre Cambridge, United Kingdom ---MOQ1035624887d46269b63be00190b5ce2c8050bc002c Content-Type: application/octet-stream; name="PHTLBC.zmatrix" Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="PHTLBC.zmatrix" Wm1hdHJpeCBnZW5lcmF0ZWQgYnkgTWVyY3VyeQ0KMS4wIDEuMCAxLjAgOTAuMCA5MC4wIDkwLjAN CiAgNDQgICAwDQogIEIgICAgICAwLjAwMDAwMDAgIDAgICAgMC4wMDAwMDAwICAwICAgIDAuMDAw MDAwMCAgMCAgICAwICAgIDAgICAgMCAgMy4wICAxLjAgICAgMSBCMSANCiAgQ2wgICAgIDEuODYz NjM1OSAgMCAgICAwLjAwMDAwMDAgIDAgICAgMC4wMDAwMDAwICAwICAgIDEgICAgMCAgICAwICAz LjAgIDEuMCAgICAyIENsMSBCMSANCiAgTiAgICAgIDEuNDY1NjM4MCAgMCAgMTEzLjc2ODM2ODEg IDAgICAgMC4wMDAwMDAwICAwICAgIDEgICAgMiAgICAwICAzLjAgIDEuMCAgIDIyIE4yIEIxIENs MSANCiAgTiAgICAgIDEuNDY3OTcxNSAgMCAgMTEyLjcxMzQwNjEgIDAgIDExOS44MjIwMjU5ICAw ICAgIDEgICAgMiAgICAzICAzLjAgIDEuMCAgIDI0IE40IEIxIENsMSBOMiANCiAgTiAgICAgIDEu 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Morales" To: "Iain Wallace" , "CCL" Subject: RE: Surfnet and Ligplot and Ligbuilder Date: Fri, 25 Oct 2002 23:27:59 -0700 Message-ID: MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0006_01C27C7E.27938CE0" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4920.2300 Importance: Normal In-Reply-To: <000a01c27c47$0b01e130$626ce286@wallaceiwork> This is a multi-part message in MIME format. ------=_NextPart_000_0006_01C27C7E.27938CE0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Dear Iain, Usually to access ftp sites via anonymous ftp you usually enter for username the word "anonymous" (without the quotation marks) and then the server asks you to enter your email address. About reaching Prof. Lai, I also experience the same thing, all email bounced back. Instead try to email Dr. Gao Yin at gao@mdl.ipc.pku.edu.cn I had to email Dr. Yin several times. For some reason their server tends to bounce back emails as well. Eventually one makes it through. I hope it helps. Best of luck, - Guillermo. ----- Dr. Guillermo A. Morales Morales Consulting E-mail: morales@combichemlab.com Website: http://www.combichemlab.com Member of the Combi-Web Consortium: http://www.combi-web.com -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On Behalf Of Iain Wallace Sent: Friday, October 25, 2002 9:53 AM To: CCL Subject: CCL:Surfnet and Ligplot and Ligbuilder Hi all, Sorry to bother you but does any one know how to get the programs ligplot and surfnet? I have tried to ftp them from ftp.biochem.ucl.ac.uk but it asks for a user name and password and I don't know how to get it. What should I do? I am also having trouble installing LigBuilder. I have downloaded the file but I cann't manage to decrypt it as I my e-mails keep getting bounced back when I e-mail Prof. Lai at lai@ipc.pku.edu.cn Does anyone know who I should e-mail ? I am a postgraduate student in TCD Thanks for your help again Iain ------=_NextPart_000_0006_01C27C7E.27938CE0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear=20 Iain,
 
Usually to access ftp sites via anonymous ftp = you=20 usually enter for username the word "anonymous" (without the quotation = marks)=20 and then the server asks you to enter your email = address.
 
About=20 reaching Prof. Lai, I also experience the same thing, all email bounced=20 back.
 
Instead try to email Dr. Gao Yin at gao@mdl.ipc.pku.edu.cn<= /FONT>
 
I had=20 to email Dr. Yin several times. For some reason their server tends to = bounce=20 back emails as well. Eventually one makes it = through.
 
I hope=20 it helps.
 
Best=20 of luck,
 
-=20 Guillermo.

-----
Dr. Guillermo A. Morales
Morales=20 Consulting
E-mail: morales@combichemlab.com
Website: http://www.combichemlab.com
= Member of=20 the Combi-Web Consortium: http://www.combi-web.com
 = =20

-----Original Message-----
From: Computational = Chemistry List=20 [mailto:chemistry-request@ccl.net]On Behalf Of Iain=20 Wallace
Sent: Friday, October 25, 2002 9:53 AM
To: = CCL
Subject: CCL:Surfnet and Ligplot and=20 Ligbuilder

Hi all,
 
Sorry to bother you but does any one = know how to=20 get the programs ligplot and surfnet?
I have tried to ftp them from ftp.biochem.ucl.ac.uk=20 but it asks for a user name and password and I don't = know
how to get it. What should I do? =
 
I am also having trouble installing = LigBuilder. I=20 have downloaded the file but I cann't manage to decrypt it as I my = e-mails=20 keep getting
bounced back when I e-mail Prof. Lai = at lai@ipc.pku.edu.cn Does anyone = know who I=20 should e-mail ?
 
I am a postgraduate student in TCD =
 
Thanks for your help = again
 
Iain
 
------=_NextPart_000_0006_01C27C7E.27938CE0-- From chemistry-request@server.ccl.net Sat Oct 26 04:37:37 2002 Received: from century.fen.bilkent.edu.tr ([139.179.97.100]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9Q8bZj29847 for ; Sat, 26 Oct 2002 04:37:35 -0400 Received: from localhost (d7992.dorm.bilkent.edu.tr [139.179.137.92]) by century.fen.bilkent.edu.tr (8.9.1/8.9.1) with ESMTP id LAA08880 for ; Sat, 26 Oct 2002 11:32:52 +0300 (EET DST) Date: Sat, 26 Oct 2002 11:37:33 +0300 Mime-Version: 1.0 (Apple Message framework v482) Content-Type: text/plain; charset=UTF-8; format=flowed Subject: error message in G98 From: Ulrike Salzner To: chemistry@ccl.net Message-Id: <2C40CAEC-E8BE-11D6-B983-00039377B832@fen.bilkent.edu.tr> X-Mailer: Apple Mail (2.482) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g9Q8bbj29850 Hello, can somebody explain the following error message in G98 to me? Two-electron integral symmetry is turned on. 1572 basis functions 2472 primitive gaussians 267 alpha electrons 267 beta electrons nuclear repulsion energy 7684.4047718364 Hartrees. One-electron integrals computed using PRISM. PrsmSu: requested number of processors reduced to: 1 ShMem 1 Linda. 4 Symmetry operations used in ECPInt. ECPInt: NShTT= 57970 NPrTT= 161938 LenC2= 18539 LenP2D= 39068. LDataN: DoStor=F MaxTD1= 4 Len= 56 LDataN: DoStor=T MaxTD1= 4 Len= 56 Number of processors reduced to 1 by ecpmxn. NBasis= 1572 RedAO= T NBF= 562 224 224 562 NBsUse= 1572 1.00D-04 NBFU= 562 224 224 562 ShPair-MaxDen allocation failure: iend,mxcore= 1357032 1345944 Error termination via Lnk1e in /usr/g98/l303.exe. Job cpu time: 0 days 0 hours 8 minutes 48.8 seconds. File lengths (MBytes): RWF= 126 Int= 0 D2E= 0 Chk= 1 Scr= 1 As seen from the second and third line, it is a pretty big job. It is an attempted DFT B3P86 geometry optimization on a conjugated π-system with c2h symmetry that will have a very small <0.2 eV energy gap. Maybe this causes the problem. The computer is a dual processor 933MHz PC with 1 Gb of memory and about 16 Gb free disk space. Can somebody tell me how to get the job running? Thanks, Ulrike Salzner