From chemistry-request@ccl.net Wed Jun 15 05:53:47 2005 Received: from ims22.stu.nus.edu.sg (ims22.stu.nus.edu.sg [137.132.14.250]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5F9rf6A008203 for ; Wed, 15 Jun 2005 05:53:42 -0400 Received: from MBOX23 ([137.132.14.234]) by ims22.stu.nus.edu.sg with Microsoft SMTPSVC(5.0.2195.6713); Wed, 15 Jun 2005 17:06:23 +0800 X-MimeOLE: Produced By Microsoft Exchange V6.0.6603.0 Content-class: urn:content-classes:message MIME-Version: 1.0 Subject: CCL: W:isotope calculations Date: Wed, 15 Jun 2005 17:06:23 +0800 Message-ID: <917268CAD5C1584A8DD36A8330E5631785C146..at..MBOX23.stu.nus.edu.sg> From: "Ma Hua" To: Dear Kono, I do the following calculation, and it works well. Have I answered = your question? Regards, Ma Hua 1. %chk=3Dformaldehyde # cbs-4m = formaldehyde = 0 1 c o 1 oc2 h 1 hc3 2 hco3 h 1 hc4 2 hco4 3 dih4 = oc2 1.450000 hc3 1.089000 hco3 109.471 hc4 1.089000 hco4 109.471 dih4 120.000 2. %chk=3Dformaldehyde #cbs-4m = formaldehyde = 0 1 c o 1 oc2 h 1 hc3 2 hco3 h 1 hc4 2 hco4 3 dih4 oc2 1.450000 hc3 1.089000 hco3 109.471 hc4 1.089000 hco4 109.471 dih4 120.000 --link1-- %chk=3Dformaldehyde #cbs-4m 0 1 298.16 0.0 0.0 12 16 2 2 Ps: I do not know what your programm exactly means. :) From chemistry-request@ccl.net Thu Jun 16 05:38:08 2005 Received: from iris.inc.bme.hu (iris.inc.bme.hu [152.66.63.5]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5G9c217032674 for < ccl.net>; Thu, 16 Jun 2005 05:38:03 -0400 Received: from dino (helo=localhost) by iris.inc.bme.hu with local-esmtp (Exim 3.36 #1 (Debian)) id 1Dipxs-0006Rr-00 for < ccl.net>; Thu, 16 Jun 2005 10:43:08 +0200 Date: Thu, 16 Jun 2005 10:43:08 +0200 (CEST) From: Szieberth Denes < iris.inc.bme.hu> To: chemistry >< ccl.net Subject: Re: CCL:cycloketones In-Reply-To: <20050615141750.65562.qmail >< web52305.mail.yahoo.com> Message-ID: < iris.inc.bme.hu> References: <20050615141750.65562.qmail >< web52305.mail.yahoo.com> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net On Wed, 15 Jun 2005, talia wrote: > Dear ccl > I want to compare expremental of vibrational frequency for the molecules > cyclopropanone,cyclobutanone,cyclopentanone,.....and cyclooctanone with result of the gaussian . > How I can recognize and assignment frequency?because I do not have expremental data for this compare. > please help me. > thanks You can find probably some of the experimental IR spectra at http://webbook.nist.gov For the visualisation and assignment of the results of the second derivative calculations made by Gaussian there are several utilities, my favorite is MOLDEN. (www.cmbi.ru.nl/molden/molden.html) cheers, Denes From chemistry-request@ccl.net Thu Jun 16 08:04:53 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5GC4rKR006343 for ; Thu, 16 Jun 2005 08:04:53 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j5GC4rHr006342 for chemistry_at_ccl.net; Thu, 16 Jun 2005 08:04:53 -0400 Date: Thu, 16 Jun 2005 08:04:53 -0400 Message-Id: <200506161204.j5GC4rHr006342_at_server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request_at_ccl.net using -f From: "Steven, , Kirk" To: chemistry_at_ccl.net X-Web-Message-Number: 050616080005-6211 Subject: W:Molecular dynamics of silica in H2O X-Spam-Status: No, score=-2.8 required=5.0 tests=ALL_TRUSTED autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hello, I want to start an MD simulation of a silica particle of size 5-10 nm in aequous solution, possibly also with a few Na+ ions floating around. I have a sample PDB file containing the structure of a silica nanoparticle, and have tried to make a box containing the nanoparticle and some water molecules using the 'genbox' utility program of GROMACS. The problem arises when defining the parameters which determine how the atoms will interact. Does anyone have a good set of general parameters for such a system ? I am aware of the the work of Wensink and Hoffmann [Langmuir 16, 7392 (2000)], but their scheme relies on a partitioning of the system into crystal, surface and water atoms and I do not know how such a partitioning could be done in my case so as to best use their parameterization. I'm not 100% tied to using GROMACS (any freely available and capable MD code will do for some initial investigations). I would be grateful for any advice on alternatives. My investigations are intended to look into the behaviour in solution of silica nanoparticles formed by polymerization in solutions of sodium silicates, including nucleation, growth, formation of charged nanoparticles (and consequently double layers) and the effect of solution pH on this process and the detailed effects on nanoparticle surface charge density. The list above is long, I realize, but I would very much appreciate some pointers on how to get started quickly into these investigations. Many thanks in advance, Steve Kirk From chemistry-request@ccl.net Thu Jun 16 06:48:26 2005 Received: from web54209.mail.yahoo.com (web54209.mail.yahoo.com [206.190.39.251]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j5GAmMVS003704 for ; Thu, 16 Jun 2005 06:48:23 -0400 Received: (qmail 1474 invoked by uid 60001); 16 Jun 2005 09:48:20 -0000 DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; h=Message-ID:Received:Date:From:Subject:To:MIME-Version:Content-Type:Content-Transfer-Encoding; b=Z/aFWkAVIyXHntJlF0rrIMoNiCg4oXhiI/u1TnZUJPuPYDaZZTGXcxpGrl3tlGSdT8B/rBmMi5QIuv3VdkcfGw+nAFS5F4sp9C6ni7XTvdFSlkgutBT0srK2dFLKfXTkTft5W68QVAwa6k7jH3uNpHcOiyQNRS3rffdT8C/n2qM= ; Message-ID: <20050616094820.1472.qmail_at_web54209.mail.yahoo.com> Received: from [139.19.34.3] by web54209.mail.yahoo.com via HTTP; Thu, 16 Jun 2005 02:48:20 PDT Date: Thu, 16 Jun 2005 02:48:20 -0700 (PDT) From: Somak Ray Subject: A question on ICM Dock To: chemistry_at_ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=1.8 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST autolearn=no version=3.0.3 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hello CCLers, I have used earlier ICM-Dock for the docking of some inhibitors. Now my license has expired but I still have retained different files comtaining the result of the dockings( eg. the *_answers.ob and *_answers.cnf files). Is there any way to view these files using ICM-Browser or ICM-Browser-Pro? I'm particularly intereseted in geeting back the conformations and their binding energies. Thanks in advance. SR __________________________________ Discover Yahoo! Use Yahoo! to plan a weekend, have fun online and more. Check it out! http://discover.yahoo.com/ From chemistry-request@ccl.net Thu Jun 16 06:04:59 2005 Received: from mail.nervianoms.com ([217.220.17.130]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5GA4vOe001612 for ; Thu, 16 Jun 2005 06:04:57 -0400 Received: from /spool/local by nervianoms.com with [XMail 1.17mod3 (Win32/Ix86) LMAIL Server] for from ; Thu, 16 Jun 2005 10:32:51 +0200 Received: from smtpout1.nervianoms.com (10.206.81.115) by nervianoms.com with [XMail 1.17mod3 (Win32/Ix86) ESMTP Server]; Thu, 16 Jun 2005 10:32:50 +0200 thread-index: AcVyTinx/VcQldKvQ++4WlnoVrS+Vw== Received: from smtpin.nervianoms.com ([10.206.81.115]) by smtpout1.nervianoms.com with Microsoft SMTPSVC(6.0.3790.0); Thu, 16 Jun 2005 10:34:08 +0200 Received: from itnerms020.itner.eu.pnu.com ([10.206.81.108]) by smtpin.nervianoms.com with Microsoft SMTPSVC(6.0.3790.0); Thu, 16 Jun 2005 10:34:08 +0200 Received: by itnerms020.itner.eu.pnu.com with Internet Mail Service (5.5.2653.19) id ; Thu, 16 Jun 2005 10:34:55 +0200 Message-ID: From: "Stouten, Pieter [Nervianoms]" To: Subject: RE: size of ligand binding pocket Date: Thu, 16 Jun 2005 10:34:50 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Content-Class: urn:content-classes:message Importance: normal Priority: normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.3790.0 X-OriginalArrivalTime: 16 Jun 2005 08:34:08.0524 (UTC) FILETIME=[29DC34C0:01C5724E] X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j5GA4xOe001618 Hello Uwe, You may want to take a look at PASS (Putative Active Sites with Spheres). Freeware executables are available at: http://www.ccl.net/cca/software/UNIX/pass/overview.html Hope this helps, Pieter ---------------- PASS (Putative Active Sites with Spheres) is a simple computational tool that uses geometry to characterize regions of buried volume in proteins and to identify positions likely to represent binding sites based upon the size, shape, and burial extent of these volumes. PASS'S utility as a predictive tool for binding site identification is tested by predicting known binding sites of proteins in the PDB using both complexed macromolecules and their corresponding apo-protein structures. The results indicate that PASS can serve as a front-end to fast docking. The main utility of PASS lies in the fact that it can analyze a moderate-size protein (~ 30 kD) in under twenty seconds, which makes it suitable for interactive molecular modeling, protein database analysis, and aggressive virtual screening efforts. As a modeling tool, PASS (i) rapidly identifies favorable regions of the protein surface, (ii) simplifies visualization of residues modulating binding in these regions, and (iii) provides a means of directly visualizing buried volume, which is often inferred indirectly from curvature in a surface representation. PASS produces output in the form of standard PDB files, which are suitable for any modeling package, and provides script files to simplify visualization in Cerius2., InsightII., MOE., Quanta., RasMol., and Sybyl.. PASS is freely available to all. -----Original Message----- From: Uwe Richter [mailto:urichter_at_jerini.de] Sent: Wednesday, June 15, 2005 3:50 PM To: CCL Subject: CCL:size of ligand binding pocket Dear CCLers, I am looking for software which is able to quantify the size/depth of ligand binding pockets of proteins? Thanks in advance, Uwe ****************************************************************************** DISCLAIMER AND CONFIDENTIAL NOTICE The information contained in this message and any attachment thereto is to be considered privileged and confidential and is intended for the addressee(s) designated. All rights related to the message itself and its attachments are reserved. If you are not the addressee, any disclosure, reproduction, distribution, on-transmission or use of this communication are strictly prohibited. If you have received this transmission in error, please notify us immediately by return email or telephone and destroy the original message. Le informazioni contenute nel presente messaggio e nei suoi allegati devono essere considerate strettamente confidenziali e riservate esclusivamente ai destinatari indicati. Sono riservati tutti i diritti relativi al messaggio e ai suoi allegati. La lettura, la riproduzione, la diffusione, la ritrasmissione di tutto quanto contenuto nel presente messaggio h consentita esclusivamente ai soggetti destinatari. Se non doveste essere tra i destinatari indicati, ovvero qualora abbiate ricevuto per errore questo messaggio Vi preghiamo di darcene comunicazione e di rimuovere il messaggio stesso e gli allegati dal Vostro sistema. From chemistry-request@ccl.net Thu Jun 16 03:38:27 2005 Received: from smtp1.iitb.ac.in (smtp2.iitb.ac.in [203.199.51.149]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j5G7cLIw026048 for ; Thu, 16 Jun 2005 03:38:23 -0400 Received: (qmail 24185 invoked from network); 16 Jun 2005 09:08:20 +0530 Received: from unknown (HELO ldns1.iitb.ac.in) (10.200.12.1) by smtp1.iitb.ac.in with SMTP; 16 Jun 2005 09:08:20 +0530 Received: (qmail 9260 invoked by uid 509); 16 Jun 2005 03:35:16 -0000 Received: from 10.200.12.43 by ldns1 (envelope-from , uid 501) with qmail-scanner-1.25 (clamdscan: 0.85.1/940. spamassassin: 3.0.2. Clear:RC:1(10.200.12.43):. Processed in 0.01908 secs); 16 Jun 2005 03:35:16 -0000 Received: from unknown (HELO gpo.iitb.ac.in) (10.200.12.43) by ldns1.iitb.ac.in with SMTP; 16 Jun 2005 03:35:16 -0000 Received: from 10.103.159.14 (SquirrelMail authenticated user dipankarroy) by gpo.iitb.ac.in with HTTP; Thu, 16 Jun 2005 09:08:19 +0530 (IST) Message-ID: <1084.10.103.159.14.1118893099.squirrel:at:gpo.iitb.ac.in> In-Reply-To: <42B0320F.4090003:at:jerini.de> References: <42B0320F.4090003:at:jerini.de> Date: Thu, 16 Jun 2005 09:08:19 +0530 (IST) Subject: Re: CCL:size of ligand binding pocket From: "Dipankar Roy" To: chemistry:at:ccl.net User-Agent: SquirrelMail/1.4.2 MIME-Version: 1.0 Content-Type: text/plain;charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Priority: 3 Importance: Normal X-Spam-Status: No, score=0.4 required=5.0 tests=DNS_FROM_RFC_ABUSE autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hi, One option that you can try is to use FADE-PADRE. It is freely available and dose a shape analysis. best wishes Dipankar > Dear CCLers, > > I am looking for software which is able to quantify the > size/depth of ligand binding pockets of proteins? > > Thanks in advance, > Uwe > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: > line > and send your message to: CHEMISTRY:at:ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST:at:ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > *********************************************** Dipankar Roy Computational Chemistry Laboratoty Dept. of Chemistry Indian Institute of Technology, Bombay India - 400076 Phone: +91-22-2576-4130(lab) *********************************************** If your life is free of any failure You are not taking risks for success From chemistry-request@ccl.net Thu Jun 16 08:58:24 2005 Received: from prserv.net (asmtp1.prserv.net [32.97.166.51]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5GCwKPc009596 for ; Thu, 16 Jun 2005 08:58:20 -0400 Received: from [127.0.0.1] (cpe-65-29-74-171.indy.res.rr.com[65.29.74.171]) by prserv.net (asmtp1) with ESMTP id <20050616125815251028221ae> (Authid: jmmckel); Thu, 16 Jun 2005 12:58:15 +0000 Message-ID: <42B17777.4090908^at^attglobal.net> Date: Thu, 16 Jun 2005 07:58:31 -0500 From: John McKelvey User-Agent: Mozilla Thunderbird 1.0.2 (Windows/20050317) X-Accept-Language: en-us, en MIME-Version: 1.0 To: Chemistry^at^ccl.net Subject: NDDO code Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net CCLers, Could anyone point me to a source for code for doing NDDO calculations as originally first suggested by Pople, et al, i.e. using Stater-orbital based 2-e integrals, either over exact Slaters, or STO-3G fits to valence orbitals? Has anyone created such a code using GAMESS or HONDO? Regards, John McKelvey From chemistry-request@ccl.net Thu Jun 16 10:38:29 2005 Received: from mcfeely.geosc.psu.edu (mcfeely.geosc.psu.edu [128.118.174.147]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5GEcOJX014580 for ; Thu, 16 Jun 2005 10:38:24 -0400 Received: from doris.psu.edu (doris.geosc.psu.edu [128.118.174.247]) by mcfeely.geosc.psu.edu (Postfix) with ESMTP id 113D74F523 for ; Thu, 16 Jun 2005 09:38:05 -0400 (EDT) Message-Id: <5.1.0.14.2.20050616093722.00b98c80^at^email.geosc.psu.edu> X-Sender: kubicki^at^email.geosc.psu.edu X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Thu, 16 Jun 2005 09:38:08 -0400 To: chemistry^at^ccl.net From: James Kubicki Subject: Re: CCL:W:Molecular dynamics of silica in H2O In-Reply-To: <200506161204.j5GC4rHr006342^at^server.ccl.net> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_2019671==_.ALT" X-Spam-Status: No, score=0.4 required=5.0 tests=HTML_10_20,HTML_MESSAGE, HTTP_ESCAPED_HOST autolearn=no version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net --=====================_2019671==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed You should look up the work of SH Garofalini. He has done extensive SiO2-H2O simulations. I'm not sure if this force field is suitable for your purposes, but it is the closest thing I've seen. At 08:04 AM 6/16/2005, you wrote: >Hello, > >I want to start an MD simulation of a silica particle of size 5-10 nm in >aequous solution, possibly also with a few Na+ ions floating around. I >have a sample PDB file containing the structure of a silica nanoparticle, >and have tried to make a box containing the nanoparticle and some water >molecules using the 'genbox' utility program of GROMACS. > >The problem arises when defining the parameters which determine how the >atoms will interact. Does anyone have a good set of general parameters for >such a system ? I am aware of the the work of Wensink and Hoffmann >[Langmuir 16, 7392 (2000)], but their scheme relies on a partitioning of >the system into crystal, surface and water atoms and I do not know how >such a partitioning could be done in my case so as to best use their >parameterization. > >I'm not 100% tied to using GROMACS (any freely available and capable MD >code will do for some initial investigations). I would be grateful for any >advice on alternatives. > >My investigations are intended to look into the behaviour in solution of >silica nanoparticles formed by polymerization in solutions of sodium >silicates, including nucleation, growth, formation of charged >nanoparticles (and consequently double layers) and the effect of solution >pH on this process and the detailed effects on nanoparticle surface charge >density. The list above is long, I realize, but I would very much >appreciate some pointers on how to get started quickly into these >investigations. > >Many thanks in advance, >Steve Kirk > > >-= This is automatically added to each message by the mailing script =- >To send e-mail to subscribers of CCL put the string CCL: on your Subject: line >and send your message to: CHEMISTRY^at^ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST^at^ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your is mail bouncing from ccl.net domain due to spam filters, please >use the Web based form from CCL Home Page >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ James Kubicki 308 Deike Bldg. Dept. of Geosciences The Pennsylvania State University University Park, PA 16802 814-865-3951 814-574-7379 (Cell) 814-863-7823 (Fax) --=====================_2019671==_.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable You should look up the work of SH Garofalini.
He has done extensive SiO2-H2O simulations.
I'm not sure if this force field is suitable for your
purposes, but it is the closest thing I've seen.

At 08:04 AM 6/16/2005, you wrote:
Hello,

I want to start an MD simulation of a silica particle of size 5-10 nm in aequous solution, possibly also with a few Na+ ions floating around. I have a sample PDB file containing the structure of a silica nanoparticle, and have tried to make a box containing the nanoparticle and some water molecules using the 'genbox' utility program of GROMACS.

The problem arises when defining the parameters which determine how the atoms will interact. Does anyone have a good set of general parameters for such a system ? I am aware of the the work of Wensink and Hoffmann [Langmuir 16, 7392 (2000)], but their scheme relies on a partitioning of the system into crystal, surface and water atoms and I do not know how such a partitioning could be done in my case so as to best use their parameterization.

I'm not 100% tied to using GROMACS (any freely available and capable MD code will do for some initial investigations). I would be grateful for any advice on alternatives.

My investigations are intended to look into the behaviour in solution of silica nanoparticles formed by polymerization in solutions of sodium silicates, including nucleation, growth, formation of charged nanoparticles (and consequently double layers) and the effect of solution pH on this process and the detailed effects on nanoparticle surface charge density. The list above is long, I realize, but I would very much appreciate some pointers on how to get started quickly into these investigations.

Many thanks in advance,
Steve Kirk


-=3D This is automatically added to each message by the mailing script =3D-
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-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

James Kubicki
308 Deike Bldg.
Dept. of Geosciences
The Pennsylvania State University
University Park, PA 16802
814-865-3951
814-574-7379 (Cell)
814-863-7823 (Fax)
 --=====================_2019671==_.ALT-- From chemistry-request@ccl.net Thu Jun 16 09:31:41 2005 Received: from pastinakel.tue.nl (pastinakel.tue.nl [131.155.2.7]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5GDVaIF011268 for ; Thu, 16 Jun 2005 09:31:36 -0400 Received: from pastinakel.tue.nl ([127.0.0.1]) by localhost (pastinakel.tue.nl [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 43512-04 for ; Thu, 16 Jun 2005 15:31:32 +0200 (CEST) Received: from stex2.campus.tue.nl (stex2.campus.tue.nl [131.155.81.192]) by pastinakel.tue.nl (Postfix) with ESMTP for ; Thu, 16 Jun 2005 15:31:32 +0200 (CEST) X-MimeOLE: Produced By Microsoft Exchange V6.0.6487.1 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Subject: CRYSTAL03 - Help needed Date: Thu, 16 Jun 2005 15:31:32 +0200 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: CRYSTAL03 - Help needed Thread-Index: AcVyd7WyAUEvOQBDRISOOy7sujDn8w== From: "Ojwang, J.G.O." To: X-Virus-Scanned: amavisd-new at tue.nl X-Spam-Status: No, score=0.0 required=5.0 tests=URG_BIZ autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j5GDVfIF011282 Dear CCLnetters, Has anyone had experience with Crystal03? I've tried to run a system but I get error messages to the effect that: (i) increase LIM007 (ii) neighbour list too big increase LIMBEC Any idea how I can do this. Futrther when I try to run a supercel I get an error message that 'file size limit exceed'. How can i increase the limit of the file size. Waiting for an urgent response from any Crystal03 informed netter. Best Regards, Ojwang' JGO Eindhoven University of Technology, The Netherlands. From chemistry-request@ccl.net Thu Jun 16 11:03:03 2005 Received: from haydn2002.u-bourgogne.fr (haydn2002.u-bourgogne.fr [193.50.50.62]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5GF2v9Z016222 for ; Thu, 16 Jun 2005 11:02:59 -0400 Received: from ADRASTEA24BFE8 (adrastea.u-bourgogne.fr [193.52.246.58]) by haydn2002.u-bourgogne.fr (8.12.11/8.12.11) with SMTP id j5GED0Uu001496 for ; Thu, 16 Jun 2005 16:13:22 +0200 Message-ID: <008e01c5727d$912cadb0$3af634c1@ADRASTEA24BFE8> From: "Patrick Senet" To: References: <200506161204.j5GC4rHr006342^at^server.ccl.net> Subject: Re: CCL:W:Molecular dynamics of silica in H2O Date: Thu, 16 Jun 2005 16:13:01 +0200 MIME-Version: 1.0 Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2900.2180 x-mimeole: Produced By Microsoft MimeOLE V6.00.2900.2180 X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hello, Please forward the answers...we are interested by starting a similar problem (silicate planar surface in water + ions). Many thanks, Patrick Senet ----- Original Message ----- From: "Steven, , Kirk" To: Sent: Thursday, June 16, 2005 2:04 PM Subject: CCL:W:Molecular dynamics of silica in H2O > Hello, > > I want to start an MD simulation of a silica particle of size 5-10 nm in > aequous solution, possibly also with a few Na+ ions floating around. I > have a sample PDB file containing the structure of a silica nanoparticle, > and have tried to make a box containing the nanoparticle and some water > molecules using the 'genbox' utility program of GROMACS. > > The problem arises when defining the parameters which determine how the > atoms will interact. Does anyone have a good set of general parameters for > such a system ? I am aware of the the work of Wensink and Hoffmann > [Langmuir 16, 7392 (2000)], but their scheme relies on a partitioning of > the system into crystal, surface and water atoms and I do not know how > such a partitioning could be done in my case so as to best use their > parameterization. > > I'm not 100% tied to using GROMACS (any freely available and capable MD > code will do for some initial investigations). I would be grateful for any > advice on alternatives. > > My investigations are intended to look into the behaviour in solution of > silica nanoparticles formed by polymerization in solutions of sodium > silicates, including nucleation, growth, formation of charged > nanoparticles (and consequently double layers) and the effect of solution > pH on this process and the detailed effects on nanoparticle surface charge > density. The list above is long, I realize, but I would very much > appreciate some pointers on how to get started quickly into these > investigations. > > Many thanks in advance, > Steve Kirk > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: > line > and send your message to: CHEMISTRY^at^ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST^at^ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > From chemistry-request@ccl.net Thu Jun 16 11:04:44 2005 Received: from simbiosys.ca ([65.18.214.160]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5GF4gKL016430 for ; Thu, 16 Jun 2005 11:04:42 -0400 Received: from phobos.simbiosys.ca (CPE00036df36d8d-CM000f9f809310.cpe.net.cable.rogers.com [69.193.210.79]) (authenticated) by simbiosys.ca (8.11.6/8.11.6) with ESMTP id j5GDX1t24886 for ; Thu, 16 Jun 2005 09:33:07 -0400 From: Aniko Simon Organization: SimBioSys Inc. To: chemistry$at$ccl.net Subject: Re: CCL:size of ligand binding pocket Date: Thu, 16 Jun 2005 09:46:03 -0400 User-Agent: KMail/1.5.3 References: <42B0320F.4090003$at$jerini.de> In-Reply-To: <42B0320F.4090003$at$jerini.de> MIME-Version: 1.0 Content-Disposition: inline Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Message-Id: <200506160946.03547.aniko$at$simbiosys.ca> X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net On June 15, 2005 09:50 am, Uwe Richter wrote: > Dear CCLers, > > I am looking for software which is able to quantify the > size/depth of ligand binding pockets of proteins? > > Thanks in advance, > Uwe > Hello Uwe, eHiTS (http://www.simbiosys.ca/ehits/) does calculate both the size (volume) and depth of all possible ligand binding pockets. This information is saved as intermediate info. One of the detected pockets is selected and used for docking later on in the program. Another tool, that provides visualization as well, is SPROUT, de-novo ligand design tool (http://www.simbiosys.ca/sprout/). The program analyses all of the binding pockets of a protein in it's cleft detection module. See description of the method here: http://www.simbiosys.ca/sprout/eccc/cangaroo.html Thanks, Regards, Aniko From chemistry-request@ccl.net Thu Jun 16 13:57:57 2005 Received: from wproxy.gmail.com (wproxy.gmail.com [64.233.184.203]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5GHvtUY025643 for ; Thu, 16 Jun 2005 13:57:55 -0400 Received: by wproxy.gmail.com with SMTP id 63so105290wri for ; Thu, 16 Jun 2005 10:57:55 -0700 (PDT) DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=beta; d=gmail.com; h=received:message-id:date:from:reply-to:to:subject:mime-version:content-type:content-transfer-encoding:content-disposition; b=r9J1872vPA9+d1fssxmDQiJxXIqHoOVDtRbvGsZ29Sn6CDdvVVUPA55//AnBavXwfeeLtLOCmVjhkTTMil3UTamcCpuX3l8r5uMFkkBnHnoOib4ooURQKjpROBc0wPWmTmELoUL6CIP2DB4YmzFUeGa8aoDZg24en4Iq56IIMR4= Received: by 10.54.55.20 with SMTP id d20mr21479wra; Thu, 16 Jun 2005 09:57:55 -0700 (PDT) Received: by 10.54.20.63 with HTTP; Thu, 16 Jun 2005 09:57:54 -0700 (PDT) Message-ID: <755a1e3b050616095744fae9e2*at*mail.gmail.com> Date: Thu, 16 Jun 2005 09:57:54 -0700 From: Pradyumna Shaakuntal Singh Reply-To: pradyu*at*u.arizona.edu To: chemistry*at*ccl.net Subject: Force Constants Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Disposition: inline X-Spam-Status: No, score=0.0 required=5.0 tests=RCVD_BY_IP autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j5GHvvUY025649 Hello, Could someone on this list please suggest how I could obtain a force-constant for a diatomic and triatomic molecule in eV/A^2 instead of mDyne/A. I am using Gaussian at the B3LYP/MP2 level. Thanks, Pradyumna From chemistry-request@ccl.net Thu Jun 16 13:07:24 2005 Received: from limicola.its.uu.se (limicola.its.UU.SE [130.238.7.33]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5GH7IK9022655 for ; Thu, 16 Jun 2005 13:07:18 -0400 Received: by limicola.its.uu.se (Postfix, from userid 205) id D075E48C7; Thu, 16 Jun 2005 18:09:44 +0200 (MSZ) Received: from limicola.its.uu.se(127.0.0.1) by limicola.its.uu.se via virus-scan id s2081; Thu, 16 Jun 05 18:09:39 +0200 Received: from vangogh.bmc.uu.se (rembrandt.bmc.uu.se [130.238.41.202]) by limicola.its.uu.se (Postfix) with ESMTP id 1F63648CE for ; Thu, 16 Jun 2005 18:09:39 +0200 (MSZ) Subject: Re: CCL:W:Molecular dynamics of silica in H2O From: David van der Spoel To: chemistry*at*ccl.net In-Reply-To: <200506161204.j5GC4rHr006342*at*server.ccl.net> References: <200506161204.j5GC4rHr006342*at*server.ccl.net> Content-Type: text/plain Date: Thu, 16 Jun 2005 18:10:25 +0200 Message-Id: <1118938225.16672.64.camel@vangogh> Mime-Version: 1.0 X-Mailer: Evolution 2.0.4 (2.0.4-4) Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net On Thu, 2005-06-16 at 08:04 -0400, Steven, , Kirk wrote: > Hello, > > I want to start an MD simulation of a silica particle of size 5-10 nm in aequous solution, possibly also with a few Na+ ions floating around. I have a sample PDB file containing the structure of a silica nanoparticle, and have tried to make a box containing the nanoparticle and some water molecules using the 'genbox' utility program of GROMACS. > > The problem arises when defining the parameters which determine how the atoms will interact. Does anyone have a good set of general parameters for such a system ? I am aware of the the work of Wensink and Hoffmann [Langmuir 16, 7392 (2000)], but their scheme relies on a partitioning of the system into crystal, surface and water atoms and I do not know how such a partitioning could be done in my case so as to best use their parameterization. Which parameters are you referring to? Force field? I have recently ported the Wensink et al. parameters to work with OPLS (in GROMACS). Contact me off the list if you want the files. > > I'm not 100% tied to using GROMACS (any freely available and capable MD code will do for some initial investigations). I would be grateful for any advice on alternatives. > > My investigations are intended to look into the behaviour in solution of silica nanoparticles formed by polymerization in solutions of sodium silicates, including nucleation, growth, formation of charged nanoparticles (and consequently double layers) and the effect of solution pH on this process and the detailed effects on nanoparticle surface charge density. The list above is long, I realize, but I would very much appreciate some pointers on how to get started quickly into these investigations. > > Many thanks in advance, > Steve Kirk > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY*at*ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST*at*ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel*at*xray.bmc.uu.se spoel*at*gromacs.org http://xray.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++