From chemistry-request@ccl.net Sat Oct 11 02:43:03 2003 Received: from smtp2.es.uci.edu (smtp2.es.uci.edu [128.200.80.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9B6gVdm016731 for ; Sat, 11 Oct 2003 02:42:32 -0400 Received: from 192.168.0.101 (vp087184.reshsg.uci.edu [128.195.87.184]) by smtp2.es.uci.edu (8.12.8/8.12.8) with ESMTP id h9B6jwul023172 for ; Fri, 10 Oct 2003 23:45:58 -0700 Date: Fri, 10 Oct 2003 23:42:17 -0700 From: Qiang Lu X-Mailer: The Bat! (v1.62r) Reply-To: Qiang Lu Organization: UCI MBB X-Priority: 3 (Normal) Message-ID: <1381204573.20031010234218.-at-.uci.edu> To: CHEMISTRY.-at-.ccl.net Subject: question about linux ssh and gview03 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-UCIrvine-MailScanner: No viruses found X-Spam-Status: No, hits=3.5 required=7.0 tests=RCVD_IN_OSIRUSOFT_COM,X_OSIRU_OPEN_RELAY version=2.55 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi CCLers, When I try to use gview03 over ssh, I always have problem(core dump). gview03 was installed on a linux machine(RH8.0). I wanted to use it on my laptop(RH 8.0) through ssh, but failed. Does anyone tried this before? -- Best regards, Qiang mailto:qiangl.-at-.uci.edu From chemistry-request@ccl.net Fri Oct 10 18:07:15 2003 Received: from mail.hamilton.edu (mail.hamilton.edu [150.209.8.98]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9AM6hdm011345 for ; Fri, 10 Oct 2003 18:06:43 -0400 Received: from conversion-daemon.mail.hamilton.edu by mail.hamilton.edu (iPlanet Messaging Server 5.2 HotFix 1.08 (built Dec 6 2002)) id <0HMK00I01AOWJI[at]mail.hamilton.edu> for chemistry[at]ccl.net; Fri, 10 Oct 2003 18:05:47 -0400 (EDT) Received: from hamilton.edu (ny-utica3b-45.aburny.adelphia.net [24.49.192.45]) by mail.hamilton.edu (iPlanet Messaging Server 5.2 HotFix 1.08 (built Dec 6 2002)) with ESMTPSA id <0HMK00EZHAPMOG[at]mail.hamilton.edu> for chemistry[at]ccl.net; Fri, 10 Oct 2003 18:05:47 -0400 (EDT) Date: Fri, 10 Oct 2003 18:06:40 -0400 From: Jenn Sturm Subject: g98 with Linda TCP on RH 9.0 To: chemistry[at]ccl.net Message-id: <06C69F1C-FB6E-11D7-8276-0003938AC910[at]hamilton.edu> MIME-version: 1.0 X-Mailer: Apple Mail (2.552) Content-type: text/plain; format=flowed; charset=US-ASCII Content-transfer-encoding: 7BIT X-Spam-Status: No, hits=3.5 required=7.0 tests=RCVD_IN_OSIRUSOFT_COM,USER_AGENT_APPLEMAIL, X_OSIRU_OPEN_RELAY version=2.55 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello, We have g98 running on a RedHat Linux 7.2 cluster with Linda 6.2 for parallel jobs. I'd like to upgrade the cluster to RedHat 9.0 so we can also use g03 on the cluster. I see on Gaussian's website that they support g03 with Linda TCP on RedHat 9.0, and that Linda TCP is backwards compatible with g98, *and* I've successfully run g98 on RedHat 9.0, but before paying for Linda TCP I'd like to confirm that it does in fact work with g98 on RedHat 9.0. Has anyone had success with that particular configuration? Thanks, Jenn Sturm +-------------------------------------------------------------------+ Jennifer Sturm System Administrator and Research Support Specialist Chemistry Department Hamilton College jsturm[at]hamilton.edu help[at]mercury.chem.hamilton.edu 315-859-4745 http://www.chem.hamilton.edu/ http://mars.chem.hamilton.edu/ +-------------------------------------------------------------------+ From chemistry-request@ccl.net Fri Oct 10 12:10:01 2003 Received: from mxout6.cac.washington.edu (mxout6.cac.washington.edu [140.142.33.20]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9AG9Tdm004073 for ; Fri, 10 Oct 2003 12:09:29 -0400 Received: from smtp.washington.edu (smtp.washington.edu [140.142.32.139]) by mxout6.cac.washington.edu (8.12.10+UW03.09/8.12.10+UW03.09) with ESMTP id h9AG9K0Y018855 for ; Fri, 10 Oct 2003 09:09:21 -0700 Received: from u.washington.edu (D-128-95-235-174.dhcp4.washington.edu [128.95.235.174]) (authenticated bits=0) by smtp.washington.edu (8.12.10+UW03.09/8.12.10+UW03.09) with ESMTP id h9AG9Kwx011421 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for ; Fri, 10 Oct 2003 09:09:20 -0700 Message-ID: <3F86D9B2.5020805[at]u.washington.edu> Date: Fri, 10 Oct 2003 09:09:22 -0700 From: Oliver Hucke User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry[at]ccl.net Subject: charmm topology file residue entry Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-0.1 required=7.0 tests=USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCLers, can somebody point me to a tool that converts a pdb HETATM residue into a RESI entry of a charmm topology file? I have already defined the atom types and charges. Now I need to build the internal coordinates (IC) part. How do you usually deal with this? Your help is very much appreciated. Best, Oliver ps.: I do not have access to Quanta, which is capable of this. I am looking for a non-commercial tool. _______________________________________ Oliver Hucke (PostDoc) Biomolecular Structure Center Dept. of Biochemistry University of Washington Health Sciences Building K-418C 1959 NE Pacific St Seattle, WA 98195 T:(206)685-7046 _______________________________________ From chemistry-request@ccl.net Fri Oct 10 13:24:58 2003 Received: from smtp.sud-chemieinc.com (srvus010.unitedcatalysts.com [208.23.162.8] (may be forged)) by server.ccl.net (8.12.8/8.12.8) with SMTP id h9AHOQdm006483 for ; Fri, 10 Oct 2003 13:24:27 -0400 Received: from 10.16.100.11 by smtp.sud-chemieinc.com (InterScan E-Mail VirusWall NT); Fri, 10 Oct 2003 13:24:14 -0400 (Eastern Daylight Time) Received: from srvkyem1.americas.sc-world.com ([10.16.100.68]) by srvkyec1.americas.sc-world.com with Microsoft SMTPSVC(5.0.2195.5329); Fri, 10 Oct 2003 13:24:18 -0400 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C38F53.55762418" X-MimeOLE: Produced By Microsoft Exchange V6.0.6375.0 Subject: generating or augmenting basis sets Date: Fri, 10 Oct 2003 13:24:17 -0400 Message-ID: <9DD56492790889439F731F5BD6DACA0047FC0E[at]srvkyem1.unitedcatalysts.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: generating or augmenting basis sets Thread-Index: AcOPU1VelR4z3pIcTQWU0Bd3iiwo6w== From: "Shobe, David" To: "CCL computational chemistry list (E-mail)" X-OriginalArrivalTime: 10 Oct 2003 17:24:18.0600 (UTC) FILETIME=[56185A80:01C38F53] X-Spam-Status: No, hits=1.5 required=7.0 tests=HTML_10_20,HTML_MESSAGE version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------_=_NextPart_001_01C38F53.55762418 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable When simulating "heavy heavy atoms" such as Pt or Te, the following = problem arises: the lack of large basis sets for these elements. What = is typically available is a pseudopotential with a double-zeta basis set = (e.g. LANL2DZ). There are papers in which a single polarization = function (d or f as appropriate) is derived for these elements. For = many calculations, this is adequate. But what if you need a larger basis set? I know people sometimes = "decontract" basis sets to add more "zetas", and that (3d) sets of = polarization functions are often derived from the single (d) function by = multiplying and dividing the exponent by 4. Are these universally = accepted methods, or are there critics? (The GAMESS manual seems a bit = critical of the multiply and divide by 4 strategy). Are there other = acceptable methods besides these? What if one wants a higher angular = momentum function (e.g. to add an f function when only s, p, and d = functions are available)? Or is all of this a waste because of inherent limitations of the = pseudopotential? At any rate it seems like only a few groups produce basis sets, and I = get the impression that it's a rather arcane area of computational = chemistry. =20 --David Shobe S=FCd-Chemie, Inc. ------_=_NextPart_001_01C38F53.55762418 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable generating or augmenting basis sets

When simulating "heavy heavy = atoms" such as Pt or Te, the following problem arises: the lack of = large basis sets for these elements.  What is typically available = is a pseudopotential with a double-zeta basis set (e.g. LANL2DZ).  = There are papers in which a single polarization function (d or f as = appropriate) is derived for these elements.  For many calculations, = this is adequate.

But what if you need a larger basis = set?  I know people sometimes "decontract" basis sets to = add more "zetas", and that (3d) sets of polarization functions = are often derived from the single (d) function by multiplying and = dividing the exponent by 4.  Are these universally accepted = methods, or are there critics?   (The GAMESS manual seems a = bit critical of the multiply and divide by 4 strategy).  Are there = other acceptable methods besides these?  What if one wants a higher = angular momentum function (e.g. to add an f function when only s, p, and = d functions are available)?

Or is all of this a waste because of = inherent limitations of the pseudopotential?

At any rate it seems like only a few = groups produce basis sets, and I  get the impression that it's a = rather arcane area of computational chemistry. 

--David Shobe
S=FCd-Chemie, Inc.


------_=_NextPart_001_01C38F53.55762418-- From chemistry-request@ccl.net Sat Oct 11 05:01:19 2003 Received: from wn1.sci.kun.nl (wn1.sci.kun.nl [131.174.8.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9B90kdm019125 for ; Sat, 11 Oct 2003 05:00:47 -0400 Received: from dialin-2.sci.kun.nl by wn1.sci.kun.nl via dialin-2.sci.kun.nl [131.174.9.2] with ESMTP id h9B90f5A002190 (8.12.10/3.58); Sat, 11 Oct 2003 11:00:41 +0200 (MEST) From: "E.L. Willighagen (Egon)" Reply-To: egonw~at~sci.kun.nl To: Barry Hardy , chemistry~at~ccl.net Subject: Re: CCL:Speaker program, Oct 17th Poster deadline - eCheminformatics 2003 virtual conference Date: Sat, 11 Oct 2003 11:00:10 +0200 User-Agent: KMail/1.5.1 References: <5.0.2.1.0.20031010131548.00a40230~at~mail.tiscalinet.ch> In-Reply-To: <5.0.2.1.0.20031010131548.00a40230~at~mail.tiscalinet.ch> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Content-Disposition: inline Message-Id: <200310111100.10663.egonw~at~sci.kun.nl> X-Spam-Status: No, hits=-2.5 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_KMAIL version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) On Friday 10 October 2003 13:16, Barry Hardy wrote: > * Speaker Program released for eCheminformatics 2003 virtual conference > > You can now view the eCheminformatics Speaker program with schedule, > speaker information and Abstracts at the following links: > > http://conferences.metalayer.net/echeminfo/logon/default.aspx?myurl=/design >/conference/html/program.htm Looks like a nice program, but I think $300 is a bit expensive for an eConference.... Egon -- PhD Molecular Representation in Chemometrics Laboratory of Analytical Chemistry http://www-cac.sci.kun.nl/people/egonw.html From chemistry-request@ccl.net Sat Oct 11 06:12:39 2003 Received: from smtp.tiscali.ch (smtp.tiscali.ch [212.40.5.52]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9BAC7dm019756 for ; Sat, 11 Oct 2003 06:12:08 -0400 Received: from avdemo.tiscalinet.ch (line-60-191-bs1.tiscali.ch [212.254.60.191]) by smtp.tiscali.ch (8.11.7/8.11.7) with ESMTP id h9BAC3G14833; Sat, 11 Oct 2003 12:12:03 +0200 Message-Id: <5.0.2.1.0.20031011112814.00a4b100~at~mail.tiscalinet.ch> X-Sender: barry.hardy~at~mail.tiscalinet.ch X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Sat, 11 Oct 2003 12:16:11 +0200 To: egonw~at~sci.kun.nl, chemistry~at~ccl.net From: Barry Hardy Subject: Re: CCL:Speaker program, Oct 17th Poster deadline - eCheminformatics 2003 virtual conference In-Reply-To: <200310111100.10663.egonw~at~sci.kun.nl> References: <5.0.2.1.0.20031010131548.00a40230~at~mail.tiscalinet.ch> <5.0.2.1.0.20031010131548.00a40230~at~mail.tiscalinet.ch> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Spam-Status: No, hits=-2.5 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello Egon Thanks for the compliment on the Cheminformatics program. I believe that a good quality virtual conference requires a dedicated team and hence either a registration fee and/or sponsorship. We are planning on having some activities on the Cheminformatics Hub which will be open to all Hub registrants without payment, but attendance at the full conference requires a reasonable fee to deliver good value to the audience and cover the costs of our team. Many of the costs and resources for organising an e-conference are actually not lower for the conference organiser compared to a physical conference, especially on the technical work done to manage the event, and to provide access at any time to the system and presentations. If you compare the cost of this registration fee with many pharmaceutical industry conference registration fees, I think I can claim that it compares very favourably in fee cost, not to mention the aspect of saved travel and hotel costs. - The registration fee also provides a one year post-conference membership to the eCheminformatics Hub, access to a monthly series of Virtual Lectures in 2004 and all archives, community and conferencing facilities - We are offering a $100 discount of the $300 fee to academic researchers - We also will be endeavoring to support bursaries for example for graduate students who wish to present a poster on their research, if it is relevant to drug discovery and good quality So in summary I am sensitive to providing good value in such a specialist area - we are endeavoring to keep the cost of these activities at a reasonable level and to also support some free-access services. Barry Hardy eCheminformatics Hub +41 61 851 0170 (office) +41 79 755 2340 (mobile) http://conferences.metalayer.net/echeminfo/ At 11:00 11/10/03 +0200, E.L. Willighagen (Egon) wrote: >On Friday 10 October 2003 13:16, Barry Hardy wrote: > > * Speaker Program released for eCheminformatics 2003 virtual conference > > > > You can now view the eCheminformatics Speaker program with schedule, > > speaker information and Abstracts at the following links: > > > > http://conferences.metalayer.net/echeminfo/logon/default.aspx?myurl=/design > >/conference/html/program.htm > >Looks like a nice program, but I think $300 is a bit expensive for an >eConference.... > >Egon > >-- >PhD Molecular Representation in Chemometrics >Laboratory of Analytical Chemistry >http://www-cac.sci.kun.nl/people/egonw.html Barry Hardy, PhD +41 61 851 0170 (office) +41 79 755 2340 (mobile) Email: barry.hardy~at~tiscalinet.ch