From chemistry-request@server.ccl.net Mon Jun 24 02:41:38 2002 Received: from hotmail.com ([64.4.20.195]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5O6fbQ23511 for ; Mon, 24 Jun 2002 02:41:38 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Sun, 23 Jun 2002 23:41:32 -0700 X-Originating-IP: [61.171.45.96] From: "Song YL" To: Subject: structure-base drug design successes Date: Mon, 24 Jun 2002 14:38:55 +0800 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0009_01C21B8C.DE1B55E0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Message-ID: X-OriginalArrivalTime: 24 Jun 2002 06:41:32.0896 (UTC) FILETIME=[2DC12E00:01C21B4A] This is a multi-part message in MIME format. ------=_NextPart_000_0009_01C21B8C.DE1B55E0 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: base64 RGVhciBDQ0xlcnMsDQogICAgICAgIFN0cnVjdHVyZS1iYXNlZCBkcnVnIGRlc2lnbixvciByYXRp b25hbCBkcnVnIGRlc2lnbiwgaGFzIGJlZW4gYSBwcm9taXNpbmcgdGVjaG5pcXVlcyBpbiB0aGUg ZGlzY292ZXJ5IGFuZCBkZXZlbG9wbWVudCBvZiBuZXcgZHJ1Z3MuDQpPZiBjb3Vyc2UsIHRoZXJl IGhhdmUgYmVlbiBhIGxvdCBvZiBzdWNjZXNzZnVsIGV4YW1wbGVzLCBzdWNoIGFzIGRydWdzIG9u IEhJViBwcm90ZWFzZSwgdGh5bWlkaW5lIHN5bnRoYXNlLlNvbWUgb2YgdGhlbSBoYXZlIHN1Y2Nl c3NmdWxseSANCmJlZW4gdXNlZCBpbiB0aGUgY2xpbmljLiANCiAgICAgICAgSG93ZXZlciwgYXMg Z3JlYXQgYWR2YW5jZW1lbnRzIGhhdmUgdGFrZW4gcGxhY2UgaW4gdGhpcyBmaWVsZCwgIHN1Y2gg YXMgRmxleFgsIEdvbGQsIEdSSUQgYW5kIGV0YywgdGhlcmUgc2hvdWxkIGJlIG1vcmUgYW5kIG1v cmUgDQpzdWNjZXNzZnVsIGV4YW1wbGVzIGluIHRoZSBzdHJ1Y3R1cmUtYmFzZWQgZHJ1ZyBkZXNp Z24gZmllbGQuICBJbiBteSB2aWV3LCB0aG91Z2ggdGhlc2UgcXVpdGUgbmV3IHNvZnR3YXJlcyBo YXZlIGJlZW4gZ2VuZXJhbGx5IHVzZWQsIHRoZXJlIA0KYXJlIGZldyBleGFtcGxlcyB0byBkZW1v bnN0cmF0ZSB0aGVpciBwb3RlbnRpYWwgaW4gdGhlIHJlYWwgZHJ1ZyBkZXNpZ24gcHJvY2Vzcy4g SSBhbSB2ZXJ5IGludGVyZXN0ZWQgaW4gdGhpcyB0b3BpYy4gSWYgeW91IGhhdmUgKG9yIGtub3cp IHNvbWUNCiBzdWNjZXNzZnVsIGV4YW1wbGVzIG9yIGV4cGVyaWVuY2VzIGluIHRoaXMgZmllbGQs IGNvdWxkIHlvdSBraW5kbHkgZW5vdWdoIHRvIHNoYXJlIHRoaXMgaW5mb3JtYXRpb24gd2l0aCBt ZT8gVGhlIG1ldGhvZCBvciBzb2Z0d2FyZXMgdXNlZCBpbiANCnRoZSBzdHVkaWVzLCBzdWNoIGFz IEZsZXhYLCBHT0xELCAgRE9DSzQsIEdSSUQsIEx1ZGkgYXJlIHdlbGxjb21lLg0KDQogICAgICAg IEkgd2lsbCBtYWtlIGEgZGV0YWlsZWQgc3VtbWFyeS4NCg0KU29uZyBZdW5sb25nLCBQaC5EDQp+ fn5+fn5+fn5+fn5+fn5+fn5+fn5+DQpEZXB0IG9mIG1lZCBjaGVtDQpTY2hvb2wgb2YgcGhhcm1h Y3kNClNlYyBNaWwgTWVkIFVuaXYNCkd1b2hlIFJvYWQsMzI1DQpTaGFuZ2hhaSwgMjAwNDMzDQpQ LiBSLiBDaGluYQ0KRS1tYWlsOnNvbmd5dW5sb25nQGhvdG1haWwuY29tDQp+fn5+fn5+fn5+fn5+ fn5+fn5+fn5+fg0K ------=_NextPart_000_0009_01C21B8C.DE1B55E0 Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: base64 PCFET0NUWVBFIEhUTUwgUFVCTElDICItLy9XM0MvL0RURCBIVE1MIDQuMCBUcmFuc2l0aW9uYWwv L0VOIj4NCjxIVE1MPjxIRUFEPg0KPE1FVEEgaHR0cC1lcXVpdj1Db250ZW50LVR5cGUgY29udGVu dD0idGV4dC9odG1sOyBjaGFyc2V0PWdiMjMxMiI+DQo8TUVUQSBjb250ZW50PSJNU0hUTUwgNi4w MC4yNjAwLjAiIG5hbWU9R0VORVJBVE9SPg0KPFNUWUxFPjwvU1RZTEU+DQo8L0hFQUQ+DQo8Qk9E WSBiZ0NvbG9yPSNmZmZmZmY+DQo8RElWPjxGT05UIHNpemU9Mj4NCjxESVY+PEZPTlQgZmFjZT0i VGltZXMgTmV3IFJvbWFuIiBzaXplPTM+RGVhciBDQ0xlcnMsPC9GT05UPjwvRElWPg0KPERJVj48 Rk9OVCBmYWNlPSJUaW1lcyBOZXcgUm9tYW4iIA0Kc2l6ZT0zPiZuYnNwOyZuYnNwOyZuYnNwOyZu YnNwOyZuYnNwOyZuYnNwOyZuYnNwOyBTdHJ1Y3R1cmUtYmFzZWQgZHJ1ZyBkZXNpZ24sb3IgDQpy YXRpb25hbCBkcnVnIGRlc2lnbiwgaGFzIGJlZW4gYSBwcm9taXNpbmcgdGVjaG5pcXVlcyBpbiB0 aGUgZGlzY292ZXJ5IGFuZCANCmRldmVsb3BtZW50IG9mIG5ldyBkcnVncy48L0ZPTlQ+PC9ESVY+ DQo8RElWPjxGT05UIGZhY2U9IlRpbWVzIE5ldyBSb21hbiIgc2l6ZT0zPk9mIGNvdXJzZSwgdGhl cmUgaGF2ZSBiZWVuIGEgbG90IG9mIA0Kc3VjY2Vzc2Z1bCBleGFtcGxlcywgc3VjaCBhcyBkcnVn cyBvbiBISVYgcHJvdGVhc2UsIHRoeW1pZGluZSBzeW50aGFzZS5Tb21lIG9mIA0KdGhlbSBoYXZl IHN1Y2Nlc3NmdWxseSA8L0ZPTlQ+PC9ESVY+DQo8RElWPjxGT05UIGZhY2U9IlRpbWVzIE5ldyBS b21hbiIgc2l6ZT0zPmJlZW4gdXNlZCBpbiB0aGUmbmJzcDtjbGluaWMuIA0KPC9GT05UPjwvRElW Pg0KPERJVj48Rk9OVCBmYWNlPSJUaW1lcyBOZXcgUm9tYW4iIA0Kc2l6ZT0zPiZuYnNwOyZuYnNw OyZuYnNwOyZuYnNwOyZuYnNwOyZuYnNwOyZuYnNwOyBIb3dldmVyLCBhcyBncmVhdCBhZHZhbmNl bWVudHMgDQpoYXZlIHRha2VuIHBsYWNlIGluIHRoaXMgZmllbGQsJm5ic3A7IHN1Y2ggYXMgRmxl eFgsIEdvbGQsIEdSSUQgYW5kIGV0YywgdGhlcmUgDQpzaG91bGQgYmUgbW9yZSBhbmQgbW9yZSA8 L0ZPTlQ+PC9ESVY+DQo8RElWPjxGT05UIHNpemU9Mz48Rk9OVCBmYWNlPSJUaW1lcyBOZXcgUm9t YW4iPnN1Y2Nlc3NmdWwgPC9GT05UPjxGT05UIA0KZmFjZT0iVGltZXMgTmV3IFJvbWFuIj5leGFt cGxlcyBpbiB0aGUgc3RydWN0dXJlLWJhc2VkIGRydWcgZGVzaWduIA0KZmllbGQuJm5ic3A7PC9G T05UPjxGT05UIGZhY2U9IlRpbWVzIE5ldyBSb21hbiI+IEluIG15IHZpZXcsIHRob3VnaCB0aGVz ZSBxdWl0ZSANCm5ldyBzb2Z0d2FyZXMgaGF2ZSBiZWVuIGdlbmVyYWxseSB1c2VkLCB0aGVyZSA8 L0ZPTlQ+PC9GT05UPjwvRElWPg0KPERJVj48Rk9OVCBzaXplPTM+PEZPTlQgZmFjZT0iVGltZXMg TmV3IFJvbWFuIj5hcmUgZmV3IGV4YW1wbGVzIHRvIGRlbW9uc3RyYXRlIA0KPC9GT05UPjxGT05U IGZhY2U9IlRpbWVzIE5ldyBSb21hbiI+dGhlaXIgcG90ZW50aWFsIDwvRk9OVD48Rk9OVCANCmZh Y2U9IlRpbWVzIE5ldyBSb21hbiI+aW4gdGhlIHJlYWwgZHJ1ZyBkZXNpZ24gcHJvY2Vzcy4gSSZu YnNwO2FtIHZlcnkgDQppbnRlcmVzdGVkIGluIHRoaXMgdG9waWMuIElmIHlvdSBoYXZlIChvciBr bm93KSBzb21lPC9GT05UPjwvRk9OVD48L0RJVj4NCjxESVY+PEZPTlQgc2l6ZT0zPjxGT05UIGZh Y2U9IlRpbWVzIE5ldyBSb21hbiI+Jm5ic3A7c3VjY2Vzc2Z1bCBleGFtcGxlczxGT05UIA0KZmFj ZT0iVGltZXMgTmV3IFJvbWFuIj4mbmJzcDtvciBleHBlcmllbmNlczwvRk9OVD48Rk9OVCANCmZh Y2U9IlRpbWVzIE5ldyBSb21hbiI+Jm5ic3A7aW4gdGhpcyA8L0ZPTlQ+PEZPTlQgZmFjZT0iVGlt ZXMgTmV3IFJvbWFuIj5maWVsZCwgDQo8L0ZPTlQ+PC9GT05UPjxGT05UIGZhY2U9IlRpbWVzIE5l dyBSb21hbiI+PEZPTlQgZmFjZT0iVGltZXMgTmV3IFJvbWFuIj5jb3VsZCANCnlvdSBraW5kbHkg ZW5vdWdoIHRvIHNoYXJlIHRoaXMgaW5mb3JtYXRpb24gd2l0aCBtZT8gVGhlIG1ldGhvZCBvciBz b2Z0d2FyZXMgDQp1c2VkIGluIDwvRk9OVD48L0ZPTlQ+PC9GT05UPjwvRElWPg0KPERJVj48Rk9O VCBzaXplPTM+PEZPTlQgZmFjZT0iVGltZXMgTmV3IFJvbWFuIj48Rk9OVCBmYWNlPSJUaW1lcyBO ZXcgUm9tYW4iPnRoZSANCnN0dWRpZXMsIDwvRk9OVD48L0ZPTlQ+PEZPTlQgZmFjZT0iVGltZXMg TmV3IFJvbWFuIj48Rk9OVCANCmZhY2U9IlRpbWVzIE5ldyBSb21hbiI+c3VjaCBhcyBGbGV4WCwg R09MRCwgPEZPTlQgDQpmYWNlPSJUaW1lcyBOZXcgUm9tYW4iPiZuYnNwO0RPQ0s0LCBHUklELCBM dWRpJm5ic3A7YXJlIDwvRk9OVD48Rk9OVCANCmZhY2U9IlRpbWVzIE5ldyBSb21hbiI+d2VsbGNv bWUuPC9GT05UPjwvRElWPjwvRk9OVD48L0ZPTlQ+PC9GT05UPg0KPERJVj48Rk9OVCBmYWNlPSJU aW1lcyBOZXcgUm9tYW4iPjwvRk9OVD4mbmJzcDs8L0RJVj4NCjxESVY+PEZPTlQgZmFjZT0iVGlt ZXMgTmV3IFJvbWFuIiANCnNpemU9Mz4mbmJzcDsmbmJzcDsmbmJzcDsmbmJzcDsmbmJzcDsmbmJz cDsmbmJzcDsgSSB3aWxsIG1ha2UgYSBkZXRhaWxlZCANCnN1bW1hcnkuPC9GT05UPjwvRElWPg0K PERJVj48Rk9OVCBmYWNlPSJUaW1lcyBOZXcgUm9tYW4iIHNpemU9Mz48L0ZPTlQ+Jm5ic3A7PC9E SVY+DQo8RElWPjxGT05UIGZhY2U9IlRpbWVzIE5ldyBSb21hbiIgc2l6ZT0zPlNvbmcgWXVubG9u ZywgUGguRDwvRk9OVD48L0RJVj4NCjxESVY+PEZPTlQgZmFjZT0iVGltZXMgTmV3IFJvbWFuIiBz aXplPTM+fn5+fn5+fn5+fn5+fn5+fn5+fn5+fjwvRk9OVD48L0RJVj4NCjxESVY+PEZPTlQgZmFj ZT0iVGltZXMgTmV3IFJvbWFuIiBzaXplPTM+RGVwdCBvZiBtZWQgY2hlbTwvRk9OVD48L0RJVj4N CjxESVY+PEZPTlQgZmFjZT0iVGltZXMgTmV3IFJvbWFuIiBzaXplPTM+U2Nob29sIG9mIHBoYXJt YWN5PC9GT05UPjwvRElWPg0KPERJVj48Rk9OVCBmYWNlPSJUaW1lcyBOZXcgUm9tYW4iIHNpemU9 Mz5TZWMgTWlsIE1lZCBVbml2PC9GT05UPjwvRElWPg0KPERJVj48Rk9OVCBmYWNlPSJUaW1lcyBO ZXcgUm9tYW4iIHNpemU9Mz5HdW9oZSBSb2FkLDMyNTwvRk9OVD48L0RJVj4NCjxESVY+PEZPTlQg ZmFjZT0iVGltZXMgTmV3IFJvbWFuIiBzaXplPTM+U2hhbmdoYWksIDIwMDQzMzwvRk9OVD48L0RJ Vj4NCjxESVY+PEZPTlQgZmFjZT0iVGltZXMgTmV3IFJvbWFuIiBzaXplPTM+UC4gUi4gQ2hpbmE8 L0ZPTlQ+PC9ESVY+DQo8RElWPjxGT05UIGZhY2U9IlRpbWVzIE5ldyBSb21hbiIgDQpzaXplPTM+ RS1tYWlsOnNvbmd5dW5sb25nQGhvdG1haWwuY29tPC9GT05UPjwvRElWPg0KPERJVj48Rk9OVCBm YWNlPSJUaW1lcyBOZXcgUm9tYW4iIA0Kc2l6ZT0zPn5+fn5+fn5+fn5+fn5+fn5+fn5+fn5+PC9G T05UPjwvRElWPjwvRk9OVD48L0RJVj48L0JPRFk+PC9IVE1MPg0K ------=_NextPart_000_0009_01C21B8C.DE1B55E0-- From chemistry-request@server.ccl.net Mon Jun 24 05:04:00 2002 Received: from simulux.us.es (IDENT:root@[150.214.145.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5O93xQ25618 for ; Mon, 24 Jun 2002 05:03:59 -0400 Received: from localhost (rafapa@localhost) by simulux.us.es (8.9.3/8.8.7) with ESMTP id LAA13237; Mon, 24 Jun 2002 11:09:38 +0200 Date: Mon, 24 Jun 2002 11:09:28 +0200 (CEST) From: "Rafael R. Pappalardo" To: Keith Refson cc: Subject: Re: CCL:Brenner potential code In-Reply-To: <15635.8926.310772.589229@kohn.nd.rl.ac.uk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 21 Jun 2002, Keith Refson wrote: > I am looking for any public domain/open source code which can handle > the Brenner potential. I found some reference to various code at > > http://www.rahul.net/pcm/brenner/ > > and > > http://www2.zyvex.com/DCAD/Software.html > > but neither of these sites appear to exist -- or at least be reachable > > from here. > > Does anyone have a pointer, or a copy of the released code? > > Keith Refson > You could try: http://www.openchem.org/brenner/ Regards, -- Dr. Rafael R. Pappalardo Dept. Quimica Fisica, Fac. de Quimica, Univ. de Sevilla. 41012-Sevilla (Spain) e-mail: rafapa@simulux.us.es From chemistry-request@server.ccl.net Mon Jun 24 10:49:08 2002 Received: from mailbox.engr.sc.edu ([129.252.21.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5OEn8Q32286 for ; Mon, 24 Jun 2002 10:49:08 -0400 Received: by mailbox.engr.sc.edu with Internet Mail Service (5.5.2655.55) id ; Mon, 24 Jun 2002 10:49:07 -0400 Message-ID: From: "WANG, YIXUAN " To: "'chemistry@ccl.net'" Subject: memory problem Date: Mon, 24 Jun 2002 10:49:05 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2655.55) Content-Type: text/plain; charset="iso-8859-1" To those who have experience on Linda, As I ran a medium-size job in single processor with requested memory=13mw, it could successfully ran even if 2 or 3 other jobs were running meanwhile. To do multi-processor calculation, I increased Nproclinda=3 ( we have four nodes, each with 2CPU) and kept the same memory request or less (8mw), initially the job really went to other nodes, however after a while it crashed regardless of jobs running or idle in other nodes. The error message read like this, Linda panic on node master.cl.usc.edu: No more memory for Tuple Space 9sbrk() failure) forrtl: error (76): IOT trap signal Fatal: ran out of heap space ntsnet: master process exited with return value 1 Thanks for your help. Yixuan Wang Department of Chemical Engineering University of South Carolina Columbia, SC 29208 From chemistry-request@server.ccl.net Mon Jun 24 11:10:37 2002 Received: from oxmail.ox.ac.uk ([129.67.1.180]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5OFAaQ00377 for ; Mon, 24 Jun 2002 11:10:37 -0400 Received: from opal.bioch.ox.ac.uk ([129.67.57.252]) by oxmail.ox.ac.uk with esmtp (Exim 3.34 #1) id 17MVUC-000381-03 for chemistry@ccl.net; Mon, 24 Jun 2002 16:10:36 +0100 Received: from quartz (quartz [129.67.57.1]) by opal.bioch.ox.ac.uk (8.12.0/8.12.0) with ESMTP id g5OFAZAH016991 for ; Mon, 24 Jun 2002 16:10:35 +0100 (BST) Date: Mon, 24 Jun 2002 16:10:35 +0100 (BST) From: Carmen Domene X-X-Sender: cdomene@quartz To: chemistry@ccl.net Subject: Cs basis set Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi. I am looking for a basis set for Cs. Thanks. -------------------------------------- Carmen Domene Lab. of Molecular Biophysics Rex Richards Building Department of Biochemistry Oxford University South Parks Road Oxford OX1 3QU U.K. Phone: +44-1865-275191 FAX: +44-1865-275182 email: carmen.domene@bioch.ox.ac.uk --------------------------------------- From chemistry-request@server.ccl.net Mon Jun 24 11:47:49 2002 Received: from cse.nd.edu (root@[129.74.25.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5OFlnQ01133 for ; Mon, 24 Jun 2002 11:47:49 -0400 Received: from dylan.cse.nd.edu (ako@dylan.cse.nd.edu [129.74.32.170]) by cse.nd.edu (8.11.2/8.11.2) with ESMTP id g5OFlkS08774 for ; Mon, 24 Jun 2002 10:47:46 -0500 (EST) Received: from localhost (ako@localhost) by dylan.cse.nd.edu (8.11.2/8.10.1) with ESMTP id g5OFliT05777 for ; Mon, 24 Jun 2002 10:47:44 -0500 (EST) Date: Mon, 24 Jun 2002 10:47:44 -0500 (EST) From: Alice NgarKit Ko To: chemistry@ccl.net Subject: charmm problems Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, I have a few questions on running charmm simulations. 1) I have this protein pdb file from protein data bank. It has a -9 charge. Do I need to add 9 Na+ to balance the charge? If yes, how and where do I add them? 2) After taking care of the charge and solvation, how long do I need to minimize the system? Or how do I know if the system is minimized? 3) After minimization and heating the system back to 300K, how kind of output files do I need to anaylsis the dyanmics? Unformatted trj? What will be the other options of output file? Thanks in advance for your time and help. Alice From chemistry-request@server.ccl.net Mon Jun 24 12:46:08 2002 Received: from crane2.cf.ac.uk ([131.251.0.25]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5OGk7Q02317 for ; Mon, 24 Jun 2002 12:46:07 -0400 Received: from thor.cf.ac.uk ([131.251.0.1]) by crane2.cf.ac.uk with esmtp (Exim 3.03 #1) id 17MWyc-0004fl-00; Mon, 24 Jun 2002 17:46:06 +0100 Received: from localhost (sacjap@localhost) by thor.cf.ac.uk (8.8.8/8.6.12) with ESMTP id RAA03426; Mon, 24 Jun 2002 17:46:06 +0100 (BST) Date: Mon, 24 Jun 2002 17:46:06 +0100 (BST) From: Jamie Platts X-Sender: sacjap@thor To: Carmen Domene cc: chemistry@ccl.net Subject: Re: CCL:Cs basis set In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Try the EMSL basis set page at: http://www.emsl.pnl.gov:2080/forms/basisform.html or http://wserv1.dl.ac.uk:800/emsl_pnl/basisform.html I think you'll have to settle for effective core potentials for Cs, ie Hay-Wadt, LANL2DZ etc. Jamie. > > Hi. > > I am looking for a basis set for Cs. > > Thanks. > >