From chemistry-request@server.ccl.net Fri Mar 28 03:42:53 2003 Received: from mr1.ucalgary.ca ([136.159.34.165]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2S8gre19250 for ; Fri, 28 Mar 2003 03:42:53 -0500 Received: from mhub1.ucalgary.ca (mhub1.ucalgary.ca [136.159.34.162]) by mr1.ucalgary.ca (Postfix) with ESMTP id DA8C77DB7; Fri, 28 Mar 2003 01:42:52 -0700 (MST) Received: from ucalgary.ca (mserve2.acs.ucalgary.ca [136.159.34.55]) by mhub1.ucalgary.ca (8.11.6/8.11.6) with ESMTP id h2S8ena12285; Fri, 28 Mar 2003 01:40:50 -0700 Received: from unknown(68.144.93.49) by mserve2.acs.ucalgary.ca via smap (V2.0) id ZZ620040; Fri, 28 Mar 2003 01:40:43 -0700 Message-ID: <3E840A98.8000805@bioboss.bio.ucalgary.ca> Date: Fri, 28 Mar 2003 01:40:56 -0700 From: Craig Shepherd User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.2) Gecko/20021202 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry@ccl.net Cc: craig@bioboss.bio.ucalgary.ca Subject: order parameters Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-MailScanner: Found to be clean X-MailScanner-Information: Please contact IT Help Desk at (403) 220-5555 for more information Hello all, I have a question regarding the calculation of 15N order parameters > from an MD simulation of a protein. I am familiar with the Lipari-Szabo model, and realize that the order parameters can be calculated from the limit of the auto-correlation function (of the 2nd Legendre polynomial) of the N-H bond vectors at infinite time, and that these should be calculated from protein structures which have been progressively fit to, say, the starting structure. My question is: what method does one use to assure that the auto-correlation function for a given bond vector has converged to some relatively constant value? The few papers I've read in which such calculations are performed don't seem to specify how this was done (I read them all some time ago, so please forgive me if I am wrong about this). Any help you can give me on the convergence question (and any other nuances or details, including the ones I claim to "understand" in the first paragraph) would be welcome. Thanks in advance, Craig Shepherd From chemistry-request@server.ccl.net Thu Mar 27 16:42:54 2003 Received: from mercury.chem.northwestern.edu ([129.105.116.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2RLgse10333 for ; Thu, 27 Mar 2003 16:42:54 -0500 Received: from mercury.chem.northwestern.edu (hutchisn@localhost [127.0.0.1]) by mercury.chem.northwestern.edu (8.12.8/8.12.8) with ESMTP id h2RLgsjn009112; Thu, 27 Mar 2003 15:42:54 -0600 (CST) Received: from localhost (hutchisn@localhost) by mercury.chem.northwestern.edu (8.12.8/8.12.8/Submit) with ESMTP id h2RLgsDf009108; Thu, 27 Mar 2003 15:42:54 -0600 (CST) X-Authentication-Warning: mercury.chem.northwestern.edu: hutchisn owned process doing -bs Date: Thu, 27 Mar 2003 15:42:54 -0600 (CST) From: Geoff Hutchison To: Yong Liang Yang cc: Subject: Re: CCL:Openbabel to convert .mmod files In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII First off, I should point out that Open Babel has its own mailing list and bug and feature trackers. You can find all of this at the website: http://openbabel.sourceforge.net/ > Currently I am using Openbabel to convert .mmod > file which contain all the information for all > the conformers(about 10 conformers per file) At the moment, Open Babel is not a direct replacement for the original Babel. In particular, there are two main limitations of the current beta version (1.100) compared to Babel 1.6. (You can still get Babel 1.6 in many places, including from ccl.net.) * Bond type perception from XYZ or other QM formats is so-so. * Multiple-molecule and multi-conformer file formats are ignored. (only the first conformer or molecule is read and translated) That said, the internal library contains support for arrays/vectors of molecules and multi-conformer information. What remains is the read/write code for the various formats and to ensure proper, correct output. We would be more than happy to receive some "donated" files in various formats to ensure proper translation and for use in our test set. Such files are typically under different copyright than the program itself, but do need to be freely distributable. Regards, -Geoff -- -Geoff Hutchison Marks/Ratner Groups (847) 491-3295 Northwestern Chemistry From chemistry-request@server.ccl.net Thu Mar 27 23:10:45 2003 Received: from mx1.ustc.edu.cn ([218.22.21.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2S4Ahe15012 for ; Thu, 27 Mar 2003 23:10:44 -0500 Received: from dxl ([202.38.82.79]) by mx1.ustc.edu.cn (8.8.7/8.8.6) with ESMTP id MAA28336 for ; Fri, 28 Mar 2003 12:00:08 +0800 Message-Id: <200303280400.MAA28336@mx1.ustc.edu.cn> Date: Fri, 28 Mar 2003 12:1:45 +0800 From: 丁迅雷 Reply-To: dxl@mail.ustc.edu.cn To: CCls Subject: how to do an excited state calculation Organization: 中国科大选键化学实验室 X-mailer: FoxMail 4.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=====000_Dragon537517742244_=====" This is a multi-part message in MIME format. --=====000_Dragon537517742244_===== Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: base64 RGVhciBDQ2xzo7oNCg0KoaGhoUhvdyB0byBjYWxjdWxhdGUgdGhlIGV4Y2l0ZWQgc3RhdGUgZm9y IHRoaXMgc3RydWN0dXJlOiANCgkgICAgICAgICAgICAgICAgICAgICBob21vLTEgICBob21vICAg bHVtbw0KCSAgICAgZ3JvdW5kIHN0YXRlOiAgIChBMSkxLCAgKEIxKTEsICAoQTEpMA0KCSAgICAg ZXhjaXRlZCBzdGF0ZTogIChBMSkwLCAgKEIxKTEsICAoQTEpMSANCgkNCg0KICAgIFRoYW5rIHlv dSBmb3IgeW91ciBoZWxwIaGhoaGhoaGhoaGhoaGhoaENCiAJCQkJDQqhoaGhoaGhoaGhoaGhoaGh oaGhoaGhoaGhoaGhRGluZyBYdW5sZWkNCqGhoaGhoaGhoaGhoaGhoaGhoaGhoaGhoaGhoaEyMDAz LTAzLTI4DQpfX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fDQpE aW5nIFh1bmxlaSwgUGguRC4gQ2FuZGlkYXRlDQpPcGVuIExhYm9yYXRvcnkgb2YgQm9uZCBTZWxl Y3RpdmUgQ2hlbWlzdHJ5DQpVbml2ZXJzaXR5IG9mIFNjaWVuY2UgJiBUZWNobm9sb2d5IG9mIENo aW5hDQpIZWZlaSwgQW5odWkgMjMwMDI2LCBQLlIuQ2hpbmENClRlbC46IDAwODYtNTUxLTM2MDM0 MTgNCkZheC46IDAwODYtNTUxLTM2MDI5NjkNCkUtbWFpbDogZHhsQG1haWwudXN0Yy5lZHUuY24N Ckh0dHA6Ly93d3cuYnNjLnVzdGMuZWR1LmNuL35keGwNCg== --=====000_Dragon537517742244_===== Content-Type: image/gif; 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Fri, 28 Mar 2003 09:06:21 -0500 Received: from exchange01.ul.pt (mail.fc.ul.pt [194.117.1.38]) by ns01.ul.pt (8.11.6/8.11.6) with ESMTP id h2SE68Y28072 for ; Fri, 28 Mar 2003 14:06:08 GMT Received: from exchange01.ul.pt ([10.101.251.101]) by exchange01.ul.pt with Microsoft SMTPSVC(5.0.2195.5329); Fri, 28 Mar 2003 14:05:58 +0000 Received: from enzimo ([194.117.40.12]) by exchange01.ul.pt with Microsoft SMTPSVC(5.0.2195.5329); Fri, 28 Mar 2003 14:05:58 +0000 From: =?iso-8859-1?Q?Gon=E7alo_Deira_Justino?= To: "CCL" Subject: reaticivity prediciton Date: Fri, 28 Mar 2003 14:06:07 -0000 Message-ID: MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0000_01C2F533.2D7429C0" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.6604 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-OriginalArrivalTime: 28 Mar 2003 14:05:58.0546 (UTC) FILETIME=[28253720:01C2F533] This is a multi-part message in MIME format. ------=_NextPart_000_0000_01C2F533.2D7429C0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit dear ccl'ers i'm trying to predict the reactivity between amino acids and several other molecules. i've the full set of rate constants for second order reactions between amino acids with, say, A and with B, and data for reaction of one or two amino acids with C. does anyone know of a formal way to predict the rate constant between the other amino acids and C? thanks to u all Gon鏰lo ______________________________ Gon鏰lo Deira Justino Biochemistry PhD student jgjustino@fc.ul.pt fax: +351 217 500 088 "there's nothing more to life than happiness!" ------=_NextPart_000_0000_01C2F533.2D7429C0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

dear ccl'ers

i'm trying to predict the = reactivity between=20 amino acids and several other molecules. i've the full set of rate = constants for=20 second order reactions between amino acids with, say, A and with B, and = data for=20 reaction of one or two amino acids with C. does anyone know of a formal = way to=20 predict the rate constant between the other amino acids and = C?

thanks to u all

Gon=E7alo

______________________________

Gon=E7alo Deira = Justino

Biochemistry PhD = student

jgjustino@fc.ul.pt

fax: +351 217 500 088

"there's nothing more to life = than=20 happiness!"

------=_NextPart_000_0000_01C2F533.2D7429C0-- From chemistry-request@server.ccl.net Thu Mar 27 15:25:17 2003 Received: from seas.marine.usf.edu ([131.247.136.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2RKPHe09019 for ; Thu, 27 Mar 2003 15:25:17 -0500 Received: from tiger (ms137dhcp111.marine.usf.edu [131.247.137.111]) by seas.marine.usf.edu (8.12.8/8.12.8) with SMTP id h2RKJfFZ022127 for ; Thu, 27 Mar 2003 15:19:41 -0500 (EST) Message-ID: <004501c2f49e$221f9360$6f89f783@seas.marine.usf.edu> From: "luo" To: Subject: Re: How to calculate bond energies Date: Thu, 27 Mar 2003 15:19:12 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0042_01C2F474.390E0900" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 Disposition-Notification-To: "luo" X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-MailScanner: Scanned This is a multi-part message in MIME format. ------=_NextPart_000_0042_01C2F474.390E0900 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable We need to compare the calculated bond energies with experiments. Now = you may using a new BDE database for the comparison, "Handbook of Bond = Dissociation Energies in Organic Compounds", CRC Press, 2002.=20 You may contact me if any question. Luo luo@seas.marine.usf.edu ------=_NextPart_000_0042_01C2F474.390E0900 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
We need to compare the calculated bond = energies=20 with experiments. Now you may using a new BDE database for the = comparison,=20 "Handbook of Bond Dissociation Energies in Organic Compounds", CRC = Press, 2002.=20
 
You may contact me if any = question.
 
Luo
luo@seas.marine.usf.edu
 
 
 
------=_NextPart_000_0042_01C2F474.390E0900-- From chemistry-request@server.ccl.net Fri Mar 28 09:50:18 2003 Received: from bureau6.utcc.utoronto.ca ([128.100.132.16]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2SEoHe07621 for ; Fri, 28 Mar 2003 09:50:17 -0500 Received: from mditdell.mdit.utoronto.ca ([128.100.251.12] HELO MditDell ident: IDENT-NOT-QUERIED [port 1050]) by bureau6.utcc.utoronto.ca with SMTP id <238508-25217>; Fri, 28 Mar 2003 09:49:58 -0500 From: "William Wei" To: "William Wei" , "Amber List" , "CCLers" Cc: Subject: Summary: Protein-Inhibitor binding affinity Date: Fri, 28 Mar 2003 09:51:30 -0500 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal In-Reply-To: Original question: I want to calculate the binding affinity of protein complex with inhibitors. Could anyone give me some suggestion? Except molecular dynamics simulation in amber, what other software is good at it? Or some reference. Thanks. Have a good day, William ----------------- Have a look to the SCORE site: http://mdl.ipc.pku.edu.cn/drug_design/work/score.html I think this is exactly what you are looking for. Rino ----------------- You can try the linear interaction energy method, based also on molecular dynamics simulations. You can find more information of the method and the software related on the Aqvist group web page: http://xray.bmc.uu.se/~aqwww/ Hope this helps, Hugo -------------------- Thank Hugo and Rino for their information! Have a good day! William From chemistry-request@server.ccl.net Fri Mar 28 16:04:45 2003 Received: from prserv.net ([32.97.166.51]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h2SL4je17947 for ; Fri, 28 Mar 2003 16:04:45 -0500 Received: from attglobal.net (dhcp065-029-083-160.indy.rr.com[65.29.83.160]) by prserv.net (asmtp1) with SMTP id <2003032821043925100dcimte> (Authid: jmmckel); Fri, 28 Mar 2003 21:04:39 +0000 Message-ID: <3E8474A4.70D17E1D@attglobal.net> Date: Fri, 28 Mar 2003 16:13:25 +0000 From: jmmckel@attglobal.net Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: It's off topic, but suggestions where to look gladly accepted Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Folks, I need an inexpensive PCI video card to use in a Linux box. [The AGP slot/board blocks air flow towards dual processors.. Suggestions? Sorry to take up bandwidth here on this. John McKelvey From jkl@ccl.net Fri Mar 28 10:05:22 2003 -0500 Return-Path: Message-Id: <200303290705.h2T75j9B027812@mail.shcnc.ac.cn> Date: Fri, 28 Mar 2003 23:6:21 +0800 From: Jinzhi Tan Reply-To: jztan@mail.shcnc.ac.cn To: "jkl@ccl.net" Subject: I want to ask questions! Dear Sir: I do something about CHARMM. I am a newer, so I encouter many questions. In the following file, I want to generate 1 psf file. In the 1.crd file, the c ordinates of ILE is right, but after run charmm, the coordinates of ILE in 2.crd is wrong, the coordinates of CD in ILE are all 9999.000, which is CD1 in 1.crd file. I don't know why. 1.crd file is generated from 1.pdb using q anta. If anyone know it, please let me know. Thank you in advance. * Polar hydrogen potential model generation of PSF from x-ray crystal * structure coordinate file. * bomb -4 ! !Read the nucleo-acid topology ! OPEN READ UNIT 2 CARD NAME ~/bin/charmm/c28a3/toppar/toph19.inp READ RTF UNIT 2 CARD CLOSE UNIT 2 ! !Read nucleo-acid parameters ! OPEN READ UNIT 2 CARD NAME ~/bin/charmm/c28a3/toppar/param19.inp READ PARAM UNIT 2 CARD CLOSE UNIT 2 OPEN READ CARD UNIT 2 NAME 1.crd READ sequ Coor UNIT 2 CLOSE UNIT 2 generate 1nql first nter last cter OPEN READ CARD UNIT 2 NAME 1.crd READ Coor card UNIT 2 CLOSE UNIT 2 OPEN write card UNIT 2 NAME 2.psf write psf CARD UNIT 2 CLOSE UNIT 2 hbuild OPEN write card UNIT 2 NAME 2.crd write coor CARD UNIT 2 CLOSE UNIT 2 stop Jinzhi Tan 2003-3-28 E-mail:jztan@mail.shcnc.ac.cn tanjinzhi@hotmail.com