From chemistry-request@server.ccl.net Tue Jul 31 02:15:26 2001 Received: from mail.iitk.ac.in ([203.200.95.130]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6V6FO531043 for ; Tue, 31 Jul 2001 02:15:25 -0400 Received: from qasid.cc.iitk.ac.in (qasid.cc.iitk.ac.in [172.31.1.16]) by mail.iitk.ac.in (8.9.3+Sun/8.9.2) with ESMTP id LAA05291 for ; Tue, 31 Jul 2001 11:44:21 +0530 (IST) Received: from apah (apah.cc.iitk.ac.in [172.31.1.6]) by qasid.cc.iitk.ac.in (8.9.2/8.9.2) with ESMTP id LAA07105 for ; Tue, 31 Jul 2001 11:32:49 +0530 (IST) Date: Tue, 31 Jul 2001 11:39:46 +0530 (IST) From: "97104 Chinmoy Ranjan UG(CHM)." X-Sender: ranjan@apah To: CHEMISTRY@ccl.net Subject: conversion to mol2 format Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear cclers, I was trying to convert a pdb file to mol2 format using babel 1.6. The job does not get done.its happening with all pdb files.. conversion to other formats like mol takes place easily. When I try to convert it to mol2 format the program just does not finish.Could any one please tell me whats the problem here. Any help is appreciated. Chinmoy Ranjan. CHINMOY RANJAN V YEAR INTEGRATED MSc CHEMISTRY INDIAN INSTITUTE OF TECHNOLOGY KANPUR From chemistry-request@server.ccl.net Tue Jul 31 09:34:12 2001 Received: from xena.oai.co.uk ([195.172.92.249]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6VDYC520537 for ; Tue, 31 Jul 2001 09:34:12 -0400 Received: by XENA with Internet Mail Service (5.5.2650.21) id <32YFR15D>; Tue, 31 Jul 2001 14:33:12 +0100 Message-ID: <5FD8C12EECBBD4119DD10002B3027B9AA843D0@GABRIELLE> From: "Charlton, Michael" To: "'chemistry@ccl.net'" Subject: ADME/Tox data Date: Tue, 31 Jul 2001 14:33:05 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" I am looking for databases and literature sources containing reliable ADME/Tox data. Preferably, it should be easy to export structure and data to other programs for analysis. I am interested in both free and purchasable sources. Can anybody help ? Thanks in advance, Michael Charlton. From chemistry-request@server.ccl.net Tue Jul 31 09:55:44 2001 Received: from quim.iq.usp.br ([143.107.52.20]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6VDtX521093 for ; Tue, 31 Jul 2001 09:55:33 -0400 Received: (from jacksong@localhost) by quim.iq.usp.br (8.9.3/8.9.3) id KAA16748; Tue, 31 Jul 2001 10:52:19 -0300 (EST) Date: Tue, 31 Jul 2001 10:52:07 -0300 (EST) From: Jackson Gois X-Sender: jacksong@quim To: chemistry@ccl.net Subject: changing aminoacids Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello everyone Does anybody know a C (open source) program to change aminoacids in pdb format (say, from ala to his) in a given protein/peptide ? Is it available ? Thanks in advance Jackson Gois jacksong@iq.usp.br jacksons@iae-sp.br From chemistry-request@server.ccl.net Tue Jul 31 13:37:55 2001 Received: from t12mail.lanl.gov ([128.165.22.99]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6VHbs526365 for ; Tue, 31 Jul 2001 13:37:54 -0400 Received: from MatCha (t12lap6.lanl.gov [128.165.22.56]) by t12mail.lanl.gov (8.9.1a/8.9.1) with SMTP id LAA07723 for ; Tue, 31 Jul 2001 11:37:52 -0600 (MDT) Content-Type: text/plain; charset="iso-8859-1" From: Matt Challacombe Reply-To: MChalla@LANL.Gov Organization: Group T-12, Los Alamos National Lab To: chemistry@ccl.net Subject: geometric basis sets Date: Tue, 31 Jul 2001 10:29:29 -0600 X-Mailer: KMail [version 1.2] MIME-Version: 1.0 Message-Id: <01073110292905.07529@MatCha> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f6VHbt526366 Hi CCLrs, It seems that the only commonly available basis set that employs a geometric progression of primitive exponents, that is an even tempered or well tempered sequence, is the well tempered basis set WTBS. This basis is quite large! For He, it is [17s]->(1s). My questions is, are there other geometric basis sets available that are not so large? Cheers, Matt -- Matt Challacombe, Ph.D. http://www.t12.lanl.gov/~mchalla/ Los Alamos National Laboratory email: MChalla@LANL.Gov Group T-12, Mail Stop B268 phone: (505) 665-5905 Los Alamos, New Mexico 87545 fax: (505) 665-3909 From chemistry-request@server.ccl.net Tue Jul 31 15:17:16 2001 Received: from mail.rpi.edu ([128.113.22.40]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6VJHG528784 for ; Tue, 31 Jul 2001 15:17:16 -0400 Received: from minghu (nidoking-32.dynamic.rpi.edu [128.113.137.201]) by mail.rpi.edu (8.11.3/8.11.3) with SMTP id f6VJHAL132630; Tue, 31 Jul 2001 15:17:11 -0400 Message-ID: <003101c119f4$b5e0ae80$c9897180@dynamic.rpi.edu> From: "Jerry Song" To: "S. Kumar Singh" Cc: , References: Subject: accessible atom or residues on protein surface Date: Tue, 31 Jul 2001 15:12:14 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Hello, Firstly, thanks for the replies from Kumar and Gert. I am sorry that I didn't make my question very clear in my previous email. I had tried the several softwares to calculate the solvent accesible area or relative %area of per atom or residue. But in order to pick out those groups on the protein surface, I also have to define a threthod value for the surface area. (for example, let is say, if the surface area of one certain residue is larger than 30%, we can assume the residue is on the protein surface.) So my question will turn into : how large will this reasonable value roughly be? ( from the view of biochemistry and chemistry) Of course I can try some arbitrary values, select out the assumed suface group and finally check them by comparing with some general-used softwares.But since I just began my work, so I am very interested in know whether any previous works/references about this question or are there any other methods instead of calculating solvent accesible areas. Thanks, Minghu From chemistry-request@server.ccl.net Tue Jul 31 17:21:22 2001 Received: from lauca.usach.cl ([158.170.64.28]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6VLLL531340 for ; Tue, 31 Jul 2001 17:21:21 -0400 Received: from lauca.usach.cl ([158.170.51.105]) by lauca.usach.cl (8.10.0.Beta12/8.10.0.Beta10) with ESMTP id f6VLINq23748 for ; Tue, 31 Jul 2001 17:18:23 -0400 (CST) Message-ID: <3B672129.D70E2F78@lauca.usach.cl> Date: Tue, 31 Jul 2001 17:20:41 -0400 From: Danilo Gonzalez X-Mailer: Mozilla 4.73 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: InsightII/UNIX Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi All! I'm working with InsightII and Discover. Anybody know how can I take only one conformation from a history file (*.his) using only UNIX command? (don't using display mode), if is possible Thanks a lot! Dr. Danilo Gonzalez University of Santiago of Chile Faculty of Chemistry and Biology Casilla 40, Correo 33, CHILE. From chemistry-request@server.ccl.net Tue Jul 31 12:52:32 2001 Received: from kineo.bowdoin.edu ([139.140.14.35]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6VGqW525240 for ; Tue, 31 Jul 2001 12:52:32 -0400 Received: from progeny ([139.140.132.181]) by kineo.bowdoin.edu (Netscape Messaging Server 4.15) with ESMTP id GHCK7J00.UMD for ; Tue, 31 Jul 2001 12:52:32 -0400 From: "Ha-Yeon Cheong" To: Subject: Gaussian98 source code and facility of parallel implementation Date: Tue, 31 Jul 2001 13:00:25 -0400 Message-ID: <000001c119e2$4b851240$b5848c8b@progeny> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0001_01C119C0.C4767F80" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.3018.1300 This is a multi-part message in MIME format. ------=_NextPart_000_0001_01C119C0.C4767F80 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit Dear folks of the CCL, Our department has recently purchased the Gaussian98 source code to implement on our 10 node Intel Pentium III Beowulf cluster (Ethernet connection) running RedHat linux 7.1. Does anybody know if the source code is parallel or SMP enabled, compiled straight out of the box? Or is it necessary to rewrite the source code in order to enable the use of %NPROC parameter in the job file? I have ran a job on the straight-from-the-box compiled version in a dual Pentium III Linux (Red Hat 6.2) machine and have run into problem which I believe to be the result of resource clash between the two processors. In this SMP machine I have let the controller determine the use of resources and it works fine now. But on the cluster I want to be able to give the %NPROC instruction from the job file because I have heard numerous reports that efficiency plateaus off and decreases around 6~8 processors. I would be grateful for any insights or suggestions. Thank you for your time. Ha Yeon Cheong Ha Yeon Cheong Bowdoin College Chemistry Intern e-mail: hcheong@bowdoin.edu ------=_NextPart_000_0001_01C119C0.C4767F80 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable

Dear folks of the = CCL,

 

Our department has recently purchased = the Gaussian98 source code

to<= /span> implement on our 10 node Intel Pentium III Beowulf cluster (Ethernet =

connection= ) running RedHat linux = 7.1. Does anybody know if the =

source code is parallel or SMP enabled, compiled straight out of the =

box= ? Or is it necessary to rewrite the source code in order to enable =

the= use of %NPROC parameter in the job file?

 

I have ran a job on the = straight-from-the-box compiled version in a dual

Pentium III Linux (Red Hat 6.2) = machine and have run into problem

which I believe to be the result of resource clash between the two =

processors= . In this SMP machine I have let the controller determine =

the= use of resources and it works fine now. But on the cluster I want to =

be<= /span> able to give the %NPROC instruction from the job file because I have =

heard numerous reports that efficiency plateaus off and decreases =

around 6~8 processors.

 

I would be grateful for any insights = or suggestions.

 

Thank you for your = time.

Ha Yeon = Cheong

 

Ha Yeon = Cheong

Bowdoin College

Chemistry = Intern

e-mail: = hcheong@bowdoin.edu

 

------=_NextPart_000_0001_01C119C0.C4767F80--