From chemistry-request@server.ccl.net Tue Nov 20 03:14:01 2001 Received: from lancelot.imb-jena.de ([192.124.248.76]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAK8E0B09848 for ; Tue, 20 Nov 2001 03:14:00 -0500 Received: (from pineda@localhost) by lancelot.imb-jena.de (SGI-8.9.3/8.8.8) id JAA29814; Tue, 20 Nov 2001 09:13:48 +0100 (CET) From: pineda@imb-jena.de (Felipe Pineda) Message-Id: <10111200913.ZM29808@lancelot.imb-jena.de> Date: Tue, 20 Nov 2001 09:13:48 +0000 In-Reply-To: "Magnus" "CCL:Appropriate docking software" (Nov 20, 1:23am) References: <007901c17159$992a5180$0b5b2cd5@sungam> X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: "Magnus" , Subject: Re: CCL:Appropriate docking software Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii hi Michel, don't forget the Flex suite of programms (http://cartan.gmd.de/flexx/) by the Lengauer group and FTDock (www.bmm.icnet.uk/docking/ftdock.html) by the Sternberg group. Another popular docking software is ICM (http://www.molsoft.com/icmpages/icmdock.htm) by Molsoft. best regards felipe -- ********************************************************************** * Felipe Pineda,PhD * * Institut fuer Molekulare Biotechnologie * * AG Theoretische Biophysik * * Beutenbergstrasse 11, Jena Vox: +49-3641-65-6491 * * Postfach 100 813, D-07708 Jena, Germany Fax: -6495 * * web: www.imb-jena.de/~pineda * ********************************************************************** ********************************************************************** * DISCLAIMER: Unless indicated otherwise, everything in this note is * * my personal opinion, not an official statement of my employer * ********************************************************************** From chemistry-request@server.ccl.net Tue Nov 20 05:58:50 2001 Received: from libra.cus.cam.ac.uk (cusexim@[131.111.8.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAKAwoB12823 for ; Tue, 20 Nov 2001 05:58:50 -0500 Received: from js252 (helo=localhost) by libra.cus.cam.ac.uk with local-smtp (Exim 3.951 #4) id 1668bv-00041E-00 for CHEMISTRY@ccl.net; Tue, 20 Nov 2001 10:58:39 +0000 Date: Tue, 20 Nov 2001 10:58:39 +0000 (GMT) From: "J. Smith" To: CHEMISTRY@ccl.net Subject: Help with NADP competitive inhibitors Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello - I wonder if someone can tell me where I can obtain a "free" list of as many NADP competitive inhibitors as possible each with a reference to a review or primary literature source. Thanks in advance Dr James Smith Department of Chemistry University of Cambridge From chemistry-request@server.ccl.net Tue Nov 20 07:55:20 2001 Received: from mail.shcnc.AC.CN ([202.127.16.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAKCtIB14581 for ; Tue, 20 Nov 2001 07:55:19 -0500 Received: from PC18 ([202.127.19.225]) by mail.shcnc.AC.CN (8.12.1/8.12.1) with SMTP id fAL3rds7009591 for ; Tue, 20 Nov 2001 19:53:39 -0800 (PST) Message-Id: <200111210353.fAL3rds7009591@mail.shcnc.AC.CN> Date: Tue, 20 Nov 2001 20:49:57 +0800 From: bxiong To: "chemistry@ccl.net" Subject: X-mailer: FoxMail 3.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Dear CCL: sorry, recently, I read some articles such as Junmei Wang's, they use the atom accessable solvation area(SA mean) as a parameter to simulation the water effect. I think may someone know a formula can add to AMBER FF function to simulation a implicit water model, so the protein (especial large protein such as HIV RT) can use this mehtod to do MD, but need not use the explicit water model. and the result also very well. Can someone know how to do it? Best regards! bxiong@mail.shcnc.ac.cn Xiong Bin Shanghai Institute of Materia Medica, C.A.S. phone:021-64311833-222(office) From chemistry-request@server.ccl.net Tue Nov 20 08:23:17 2001 Received: from mail.takas.lt ([212.59.31.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAKDNHB15178 for ; Tue, 20 Nov 2001 08:23:17 -0500 Received: from olegas ([212.59.29.195]) by mail.takas.lt with Microsoft SMTPSVC(5.0.2195.2966); Tue, 20 Nov 2001 15:20:03 +0200 Message-ID: <000d01c171ce$ea65b420$c31d3bd4@olegas> From: "Olegas Eicher-Lorka" To: Subject: Mysterious G98W output Date: Tue, 20 Nov 2001 14:52:10 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0009_01C171D2.EECE68A0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 X-OriginalArrivalTime: 20 Nov 2001 13:20:03.0876 (UTC) FILETIME=[10952E40:01C171C6] This is a multi-part message in MIME format. ------=_NextPart_000_0009_01C171D2.EECE68A0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCLers, When doing B3LYP Opt's (using #P) we've only recently started to get = this in the output file: Isotropic Fermi Contact Couplings Atom a.u. MegaHertz Gauss 10(-4) = cm-1 1 C(13) 0.00908 10.21192 3.64387 = 3.40633 2 C(13) -0.00326 -3.66731 -1.30859 = -1.22328 3 H 0.00155 6.93828 2.47575 = 2.31436 4 H 0.00017 0.77599 0.27689 = 0.25884 5 H 0.00017 0.77424 0.27627 = 0.25826 6 S(33) 0.18303 62.86418 22.43151 = 20.96923 7 H 0.00016 0.73397 0.26190 = 0.24483 8 H 0.00017 0.73965 0.26392 = 0.24672 9 Cu(63) 0.89938 1066.75970 380.64649 = 355.83273 10 Cu(63) 0.89702 1063.96061 379.64770 = 354.89906 Just one simple question... what exactly is all of this, it looks a bit = 'NMRish" is it? Thanks Olegas ------=_NextPart_000_0009_01C171D2.EECE68A0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear CCLers,
 
When doing B3LYP Opt's (using #P) we've only = recently started=20 to get this in the output file:
 
          &nbs= p;           =20 Isotropic Fermi Contact Couplings
    =20 Atom           &nb= sp;    =20 a.u.      =20 MegaHertz      =20 Gauss      10(-4) cm-1
   1 =20 C(13)           &n= bsp; =20 0.00908     =20 10.21192      =20 3.64387       3.40633
   = 2 =20 C(13)           &n= bsp;=20 -0.00326      = -3.66731     =20 -1.30859      -1.22328
   3 =20 H            =      =20 0.00155      =20 6.93828      =20 2.47575       2.31436
   = 4 =20 H            =      =20 0.00017      =20 0.77599      =20 0.27689       0.25884
   = 5 =20 H            =      =20 0.00017      =20 0.77424      =20 0.27627       0.25826
   = 6 =20 S(33)           &n= bsp; =20 0.18303      = 62.86418     =20 22.43151      20.96923
   7 =20 H            =      =20 0.00016      =20 0.73397      =20 0.26190       0.24483
   = 8 =20 H            =      =20 0.00017      =20 0.73965      =20 0.26392       0.24672
   = 9 =20 Cu(63)           &= nbsp;=20 0.89938    1066.75970    =20 380.64649     355.83273
  10 =20 Cu(63)           &= nbsp;=20 0.89702    1063.96061    =20 379.64770     354.89906
 
Just one simple question... what exactly is all of = this, it=20 looks a bit 'NMRish" is it?
 
Thanks
 
Olegas

 ------=_NextPart_000_0009_01C171D2.EECE68A0-- From chemistry-request@server.ccl.net Tue Nov 20 00:44:47 2001 Received: from mail.shcnc.AC.CN ([202.127.16.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAK5ijB07475 for ; Tue, 20 Nov 2001 00:44:45 -0500 Received: from PC18 ([202.127.19.225]) by mail.shcnc.AC.CN (8.12.1/8.12.1) with SMTP id fAKKh6s7006093 for ; Tue, 20 Nov 2001 12:43:06 -0800 (PST) Message-Id: <200111202043.fAKKh6s7006093@mail.shcnc.AC.CN> Date: Tue, 20 Nov 2001 13:38:23 +0800 From: bxiong To: "chemistry@ccl.net" Subject: X-mailer: FoxMail 3.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Dear CCLs: I'm sorry. May be I not clarify my question. I want simulation the large protein, Beacause the computational expensive is very high. so I only simulate the protein but add the water effect with the SA model. but I do not know how to do. Can someone help me to add WHAT SA model and HOW to add it to AMBER FF ? thanks very much!! ( I do not want use the simple distance dependent dielectric such as 4r) any suggestion and reference will be helpful!! Best regards! bxiong@mail.shcnc.ac.cn Xiong Bin Shanghai Institute of Materia Medica, C.A.S. phone:021-64311833-222(office) From chemistry-request@server.ccl.net Tue Nov 20 10:13:12 2001 Received: from mail.shcnc.AC.CN ([202.127.16.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAKFDAB18173 for ; Tue, 20 Nov 2001 10:13:11 -0500 Received: from pc6 ([202.127.19.246]) by mail.shcnc.AC.CN (8.12.1/8.12.1) with SMTP id fAL6BVs7010515 for ; Tue, 20 Nov 2001 22:11:31 -0800 (PST) Message-Id: <200111210611.fAL6BVs7010515@mail.shcnc.AC.CN> Date: Tue, 20 Nov 2001 23:13:42 +0800 From: Xiaoying Xu To: "chemistry@ccl.net" Subject: free energy component analysis X-mailer: FoxMail 3.1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Dear Pro.: I met problems in analyse the GIBBS result in amber6. I want to do some "free energy component analysis" because it can help me understand the contribution of individual residues to the total energy change. But I have no idea of using it.Any hints about it are most welcome! Thanks in advance Xiaoying Xu xyxu@mail.shcnc.ac.cn From chemistry-request@server.ccl.net Tue Nov 20 10:25:48 2001 Received: from bute.st-andrews.ac.uk ([138.251.12.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAKFPlB18453 for ; Tue, 20 Nov 2001 10:25:47 -0500 Received: from localhost (im17@localhost) by bute.st-andrews.ac.uk (8.9.1a/8.9.1) with SMTP id PAA12263; Tue, 20 Nov 2001 15:17:33 GMT Date: Tue, 20 Nov 2001 15:17:31 +0000 (GMT) From: Ibrahim Moustafa X-Sender: im17@st-andrews.ac.uk To: bxiong cc: "chemistry@ccl.net" Subject: Re: CCL:X-mailer: FoxMail 3.0 beta 2 [cn] In-Reply-To: <200111210353.fAL3rds7009591@mail.shcnc.AC.CN> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Can you send more information about the articles u mentioned? Titles? and Journals? Thanks, Ibrahim Name :Ibrahim M.Moustafa Mail address :Center for Biomolecular Science, BIOMOLECULAR SCIENCE BUILDING, North Haugh,St-Andrews, Fife,KY16 9ST Scotland,U.K. Tel :+44(0)1334-467257 E-mail :im17@st-andrews.ac.uk On Tue, 20 Nov 2001, bxiong wrote: > Dear CCL: > sorry, recently, I read some articles such as Junmei Wang's, they use the atom accessable solvation area(SA mean) as a parameter to simulation the water effect. I think may someone know a formula can add to AMBER FF function to simulation a implicit water model, so the protein (especial large protein such as HIV RT) can use this mehtod to do MD, but need not use the explicit water model. and the result also very well. > Can someone know how to do it? > > > > > Best regards! > > bxiong@mail.shcnc.ac.cn > > Xiong Bin > Shanghai Institute of Materia Medica, C.A.S. > phone:021-64311833-222(office) > > > > -= 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 Nov 20 14:34:16 2001 Received: from mserv.itpa.lt ([193.219.53.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAKJYEB24315 for ; Tue, 20 Nov 2001 14:34:15 -0500 Received: from localhost (tamulis@localhost) by mserv.itpa.lt (8.11.6/8.11.0) with ESMTP id fAKJY0L89528 for ; Tue, 20 Nov 2001 21:34:00 +0200 (EET) (envelope-from tamulis@itpa.lt) Date: Tue, 20 Nov 2001 21:33:59 +0200 (EET) From: Arvydas Tamulis To: Subject: Help with Gaussian formchk In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Colleagues, We wish to do according Gaussian description in www.gaussian.com: PROMPT 1% formchk acrolein.chk Read checkpoint file Write formatted checkpoint file --------------- Unfortunately in CRAY we did not received acrolein.fchk file: pink 47% formchk acrol.chk Bad file opened by FileIO: Unit=2 NFiles= 0 MaxFil= 213. FILEIO: IOPER= 9 IFILNO(1)= 2 LEN= 0 IPOS= 0 Q= 149763 Error termination in NtrErr: NtrErr called from FileIO. Operand range error Beginning of Traceback: Started from address 147470a in routine 'kill'. Called from line 2057 (address 4550d) in routine 'GAUABT'. Called from line 22 (address 34225d) in routine 'NTRERR'. Called from line 1264 (address 22736c) in routine 'FILEIO'. Called from line 28 (address 26071a) in routine 'FOPEN'. Called from line 58 (address 41620d) in routine 'STARCK'. Called from line 16 (address 352d) in routine 'FORMCH'. Called from line 360 (address 124674d) in routine '$START$'. End of Traceback. Operand range error (core dumped) _________________________________ Maybe you can say why we received bad result? Thanking your in advance. With best regards, Arvydas Tamulis ***************************************** Arvydas Tamulis Doctor of Natural Sciences, senior research fellow Institute of Theoretical Physics and Astronomy, Theoretical Molecular Electronics Research Group, A. Gostauto 12, Vilnius 2600, Lithuania e-mail: TAMULIS@ITPA.lt; WEBsite: http://www.itpa.lt/~tamulis/ fax: +(370-2)-225361 or +(370-2)-224694 Phone: +(370-2)-620861 Home address: Didlaukio 27-40, Vilnius 2057, Lithuania Phone: +370-9919397 From chemistry-request@server.ccl.net Tue Nov 20 12:05:13 2001 Received: from web12905.mail.yahoo.com ([216.136.174.72]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fAKH5DB20870 for ; Tue, 20 Nov 2001 12:05:13 -0500 Message-ID: <20011120170502.65197.qmail@web12905.mail.yahoo.com> Received: from [144.32.180.54] by web12905.mail.yahoo.com via HTTP; Tue, 20 Nov 2001 17:05:02 GMT Date: Tue, 20 Nov 2001 17:05:02 +0000 (GMT) From: =?iso-8859-1?q?Meike=20Reinhold?= Subject: B3LYP s B3P86 To: ccl MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CClers, I am looking for papers discussing the comparison of B3LYP vs B3P86 in transition metal systems (first or second row only). I am especially interested in their ability to calulate structural data accurately. Any hints would be appreciated, Meike reinhold ===== Meike Reinhold Chemistry Department University of York UK __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com From chemistry-request@server.ccl.net Tue Nov 20 15:57:57 2001 Received: from hartree.chem.kuleuven.ac.be ([134.58.49.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAKKvuB25950 for ; Tue, 20 Nov 2001 15:57:56 -0500 Received: from localhost (kiran@localhost) by hartree.chem.kuleuven.ac.be (8.9.0/8.9.0) with ESMTP id VAA29180 for ; Tue, 20 Nov 2001 21:56:53 +0100 Date: Tue, 20 Nov 2001 21:56:52 +0100 (NFT) From: Kiran Boggavarapu To: chemistry@ccl.net Subject: weak H-bonding In-Reply-To: <20011120170502.65197.qmail@web12905.mail.yahoo.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CClers, Probably it is well establised that DFT is NOT good for h-bonding studies. There are some reports though, that the geometires are good but not the energy. My question is, is it OK, if one does MP2 energy calculations (singlepoint) at DFT geometries say B3LYP or other (MP2/xxx//DFT/xxx). Are there any studies (published papers) to suggest this? I do also notice that DFT with small basis set say 6-31g** gives better(?) resutls compared to BIG basis set, say 6-311+G** (it may not be really big, but DFT qucikly converges to basis set limit). I appreciate any help in this regard Kiran Boggavarapu KUleuven