From chemistry-request@server.ccl.net Thu Feb 13 05:03:49 2003 Received: from ns1.tudelft.nl ([130.161.180.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1DA3mx06325 for ; Thu, 13 Feb 2003 05:03:49 -0500 Received: from CONVERSION-DAEMON.mailhost2.tudelft.nl by mailhost2.tudelft.nl (PMDF V6.1-1 #40925) id <0HA800401RY7FN@mailhost2.tudelft.nl> for chemistry@ccl.net; Thu, 13 Feb 2003 11:03:47 +0100 (MET) Received: from listserv.tudelft.nl (listserv.tudelft.nl [130.161.180.33]) by mailhost2.tudelft.nl (PMDF V6.1-1 #40925) with ESMTP id <0HA800LILRY6D4@mailhost2.tudelft.nl> for chemistry@ccl.net; Thu, 13 Feb 2003 11:03:43 +0100 (MET) Received: from mail.dct.tudelft.nl (tnw-dct1.dct.tudelft.nl [130.161.196.201]) by listserv.tudelft.nl (8.12.5/8.12.5) with ESMTP id h1DA3gsA003894 for ; Thu, 13 Feb 2003 11:03:42 +0100 (MET) Received: from TNW-DCT1/SpoolDir by mail.dct.tudelft.nl (Mercury 1.48); Thu, 13 Feb 2003 11:03:42 +0200 Received: from SpoolDir by TNW-DCT1 (Mercury 1.48); Thu, 13 Feb 2003 11:03:34 +0200 Date: Thu, 13 Feb 2003 11:03:29 +0100 From: Stefan Bromley Subject: G98 vibrational spectra To: chemistry@ccl.net Message-id: <3E4B7A4E.10027.F3C0F67@localhost> Organization: Delft University of Technology (TNW-DCT) MIME-version: 1.0 X-Mailer: Pegasus Mail for Windows (v4.02) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Content-description: Mail message body Priority: normal Dear all, does anyone know of a program to produce variably-gaussian-broadened IR spectra from the output of a G98 frequency calculation. Viewmol 2.3, which should have this facility, does not seem to accept my g89 output files. Thanks, Stefan ________________________________________________________ Dr Stefan T. Bromley Laboratory of Applied Organic Chemistry and Catalysis DelftChemTech, Delft University of Technology Julianalaan 136, 2628 BL Delft The Netherlands Phone : + 31 1527 89418 e-mail : S.T.Bromley@tnw.tudelft.nl ________________________________________________________ From chemistry-request@server.ccl.net Wed Feb 12 11:42:16 2003 Received: from nature.Berkeley.EDU ([128.32.175.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1CGgGx06921 for ; Wed, 12 Feb 2003 11:42:16 -0500 Received: from localhost (localhost [127.0.0.1]) by nature.Berkeley.EDU (Postfix) with ESMTP id AA67426126E for ; Wed, 12 Feb 2003 08:42:15 -0800 (PST) Received: from nature.Berkeley.EDU ([127.0.0.1]) by localhost (nature.Berkeley.EDU [127.0.0.1:10024]) (amavisd-new) with ESMTP id 16709-08 for ; Wed, 12 Feb 2003 08:42:14 -0800 (PST) Received: from nature.berkeley.edu (localhost [127.0.0.1]) by nature.Berkeley.EDU (Postfix) with SMTP id 9922B26125F for ; Wed, 12 Feb 2003 08:42:14 -0800 (PST) Received: from 128.32.27.14 (SquirrelMail authenticated user moconnor) by nature.berkeley.edu with HTTP; Wed, 12 Feb 2003 08:42:14 -0800 (PST) Message-ID: <1198.128.32.27.14.1045068134.squirrel@nature.berkeley.edu> Date: Wed, 12 Feb 2003 08:42:14 -0800 (PST) Subject: Cerius2 question From: To: "computational chemistry" X-Priority: 3 Importance: Normal X-Mailer: SquirrelMail (version 1.2.10) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-new Hello, CCL folks: I am just starting to use Cerius2 and cannot figure out from the manuals two points: 1.) How can I resume a run, so as to have it append a continued optimization on a structure that did not converge? 2.) How can I select a structure from within a run and tell the resume job to pick up and reoptimize that particular structure. I am working with Version 4.0. Thanks in advance for any help. Mary O'Connor,Ph.D. UC Berkeley From chemistry-request@server.ccl.net Thu Feb 13 08:44:59 2003 Received: from camdmail01.cam.accelrys.com ([192.190.183.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1DDixx10438 for ; Thu, 13 Feb 2003 08:44:59 -0500 To: Cc: "computational chemistry" Subject: Re: CCL:Cerius2 question MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.11 July 24, 2002 Message-ID: From: vmilman@accelrys.com Date: Thu, 13 Feb 2003 13:44:57 +0000 X-MIMETrack: Serialize by Router on camdmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 02/13/2003 01:44:58 PM, Serialize complete at 02/13/2003 01:44:58 PM Content-Type: text/plain; charset="us-ascii" Dear Mary, You'd have to be more specific about the tools from Cerius2 that you use to optimize your structures. The answer will be different for different energy servers in Cerius2 (force fields, quantum, etc.) Yours ============================================================= Victor Milman * Fellow Accelrys Inc * tel: (01223) 228500/228619 334 Science Park * fax: (01223) 228501 Cambridge CB4 0WN * tel. from abroad: +44 1223 228500 UK * e-mail: vmilman@accelrys.com ============================================================= Sent by: "Computational Chemistry List" 12/02/2003 16:42 To: "computational chemistry" cc: Subject: CCL:Cerius2 question Hello, CCL folks: I am just starting to use Cerius2 and cannot figure out from the manuals two points: 1.) How can I resume a run, so as to have it append a continued optimization on a structure that did not converge? 2.) How can I select a structure from within a run and tell the resume job to pick up and reoptimize that particular structure. I am working with Version 4.0. Thanks in advance for any help. Mary O'Connor,Ph.D. UC Berkeley -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Thu Feb 13 09:49:41 2003 Received: from ktaemail01.villa-bosch.de ([212.126.215.56]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1DEnex11827 for ; Thu, 13 Feb 2003 09:49:40 -0500 Received: from eml.villa-bosch.de ([212.126.215.53]) by ktaemail01.villa-bosch.de with Microsoft SMTPSVC(5.0.2195.2966); Thu, 13 Feb 2003 15:47:48 +0100 Message-ID: <3E4BB07C.1010205@eml.villa-bosch.de> Date: Thu, 13 Feb 2003 15:49:32 +0100 From: DSMM User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.1) Gecko/20020826 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry@ccl.net, wade@eml.villa-bosch.de, dsmm@eml.villa-bosch.de Subject: DSMM-Database of Simulated Molecular Motions Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-OriginalArrivalTime: 13 Feb 2003 14:47:48.0390 (UTC) FILETIME=[E05DC460:01C2D36E] Dear CCLers, If you are interested in finding movies resulting from biomolecular simulation studies, please take a look at this new website: http://projects.villa-bosch.de/mcm/database/dsmm where you will find: "DSMM: a Database of Simulated Molecular Motions". You can read about it in Finocchiaro, G. , Wang, T., Hoffmann, R., Gonzalez, A., Wade, R.C. Nucleic Acids Research, 2003, 31, 456. at: http://nar.oupjournals.org/cgi/content/abstract/31/1/456. Please do submit your own molecular movies and email your feedback to dsmm@eml.villa-bosch.de. Ting Wang and Rebecca Wade European Media Laboratory, Heidelberg dsmm@eml.villa-bosch.de From chemistry-request@server.ccl.net Thu Feb 13 15:59:49 2003 Received: from ns0.scripps.edu ([192.42.82.58]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1DKxmx19805 for ; Thu, 13 Feb 2003 15:59:49 -0500 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns0.scripps.edu (8.11.6/TSRI-4.1rx) with SMTP id h1DKxn806406 for ; Thu, 13 Feb 2003 12:59:49 -0800 (PST) Received: from relay2.scripps.edu(137.131.200.30) by antigen.scripps.edu via csmap id 20342; Thu, 13 Feb 2003 12:52:37 -0800 (PST) Received: from gage.scripps.edu (gage.scripps.edu [137.131.252.115]) by relay2.scripps.edu (8.11.6/TSRI-4.2rAV) with ESMTP id h1DKxcC09426; Thu, 13 Feb 2003 12:59:38 -0800 (PST) Received: from gage (localhost [127.0.0.1]) by gage.scripps.edu (8.9.2/TSRI-3.0.1) with ESMTP id MAA07915; Thu, 13 Feb 2003 12:32:33 -0800 (PST) Message-Id: <200302132032.MAA07915@gage.scripps.edu> To: "CUI, Guanglei" , chemistry@ccl.net Cc: bashford@scripps.edu Subject: Re: CCL:MEAD pKa calculations In-Reply-To: Your message of "Sun, 09 Feb 2003 16:46:34 EST." Date: Thu, 13 Feb 2003 12:32:32 -0800 From: Don Bashford >>>>> "CUI" == CUI, Guanglei writes: CUI> Dear CCL readers, I'm trying to use MEAD to calculate pKa of CUI> three residues in a ligand binding site. The structure has CUI> been minimized with AMBER force field with explicit CUI> solvent. The charges of these residues have been derived from CUI> RESP calculations. All needed files are created and multiflex CUI> calculation used epsin = 4.0. After the calculation, the CUI> intrinsic pKas of two residues are very surprising. So here's CUI> my questions: Hopefully you've used a fine grid of 0.25 Ang or so centered on "center of interest". CUI> 1. What could be reasons that the self interactions for CUI> residue UNK and LYS are very big. Probably because the accessibility of these residues to solvent is low. This tends to disfavor the charged states, and therefore lowers pKint for Lys, and raises it for things like Asp and Glu. CUI> 2. During the multiflex CUI> calculation, I was warned of "vertex found with count = 2" CUI> three times. How should I deal with this? This is almost certainly harmless. CUI> 3. Do I need to CUI> include explicit solvent molecules in the calculation, CUI> generally speaking? The binding site is not completely CUI> buried. People have done this both ways. It can be argued that keeping crystallographic waters is more "detailed", but on the other hand, when the ionization state of a residue changes these waters may move or reorient, and a calculation that regards them as having fixed coordinates will not capture this. A blob of high dielectric can at least repolarize! In my experience, ordinary protein residue pKa's are not much improved by including crystallographic waters, and may even get a bit worse. However, for multivalent things like metal centers, an explicit hydration shell helps, because the hydration shell is tightly bound and a singe change change doesn't really re-orient it so much. CUI> 4. LYS (protonated) has 3 equivalent hydrogens. It's CUI> not very clear to me which one should be zero charged in CUI> LYS.st file. My guess is it won't make so much difference, but why not try it all three ways? CUI> Here're the .summ file. Sorry for the lengthy CUI> description. Any suggestions are welcome. Thanks in advance. CUI> site name pKmod delta self delta back pkint CUI> UNK-259 7.8 23.1134 -5.41211 25.5013 CUI> LYS-162 10.4 -11.4993 1.32968 0.23042 CUI> TYR-155 9.6 0.694971 -1.28149 9.01348 What is UNK? I'll assume it's negatively charged. It's delta self is indeed quite big. It may be deeply buried. It's charge may be very compact or large (-2?). The delta self you get is rather typical of a buried lysine. Do UNK and Lys interact strongly? (see the .g file) If so, the favorable charge-charge interaction may stabilize the charge pair in spite of the large delta self terms. I've seen such things happen, for example in bR (Spassov et al., 2001, JMB 312:203). Cheers, Don Bashford From chemistry-request@server.ccl.net Thu Feb 13 23:36:16 2003 Received: from ilion.bio.sunysb.edu ([129.49.94.22]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1E4aGx27797 for ; Thu, 13 Feb 2003 23:36:16 -0500 Received: from dh094-148.csb.sunysb.edu (094-148.csb.sunysb.edu [129.49.94.148]) by ilion.bio.sunysb.edu (SGI-8.9.3/8.9.3) with ESMTP id XAA36650; Thu, 13 Feb 2003 23:42:28 -0500 (EST) Date: Thu, 13 Feb 2003 23:29:23 -0500 (EST) From: "CUI, Guanglei" X-X-Sender: cuigl@dh094-148.csb.sunysb.edu To: Don Bashford cc: chemistry@ccl.net Subject: Re: CCL:MEAD pKa calculations In-Reply-To: <200302132032.MAA07915@gage.scripps.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Thanks for the reply. On Thu, 13 Feb 2003, Don Bashford wrote: > Hopefully you've used a fine grid of 0.25 Ang or so centered on > "center of interest". Yes, I did so, focusing to residue UNK, which is of my interest. It's neutral and has one phenol group. > > Probably because the accessibility of these residues to solvent is > low. This tends to disfavor the charged states, and therefore lowers > pKint for Lys, and raises it for things like Asp and Glu. All three residues are inside of the protein with no solvent accessibility. > > > My guess is it won't make so much difference, but why not try it all > three ways? One of the three is different from the other two. pkint is calculated around 8. Very interesting ... > > What is UNK? I'll assume it's negatively charged. It's delta self is > indeed quite big. It may be deeply buried. It's charge may be very > compact or large (-2?). The delta self you get is rather typical of a > buried lysine. Do UNK and Lys interact strongly? (see the .g file) > If so, the favorable charge-charge interaction may stabilize the > charge pair in spite of the large delta self terms. I've seen such > things happen, for example in bR (Spassov et al., 2001, JMB 312:203). UNK is triclosan. It's neutral. The phenol hydroxyl hydrogen is hydrogen-bonded to the TYR in hydrogen-added crystal structure. The LYS is the only titratable group sticking inside of the protein. From the great impact of hydrogen atoms of the LYS, I guess the same effect could happen to UNK too. Here's the .g file. All terms are fairly small. 1 1 0.000000e+00 1 2 2.158370e-02 1 3 4.047996e-02 2 1 2.158370e-02 2 2 0.000000e+00 2 3 2.034296e-02 3 1 4.047996e-02 3 2 2.034296e-02 3 3 0.000000e+00 > > Cheers, > Don Bashford > > -- Guanglei Cui Dept. of Chemistry SUNY at Stony Brook Stony Brook, NY 11790