From chemistry-request@ccl.net Sun Oct 5 09:39:03 2003 Received: from sunchem.chem.uga.edu (sunchem.chem.uga.edu [128.192.5.2]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h95DcW59009641 for ; Sun, 5 Oct 2003 09:38:32 -0400 Received: (qmail 17183 invoked by uid 728); 5 Oct 2003 13:36:01 -0000 Received: from localhost (sendmail-bs@127.0.0.1) by localhost with SMTP; 5 Oct 2003 13:36:01 -0000 Date: Sun, 5 Oct 2003 09:36:01 -0400 (EDT) From: Zhi-Xiang Wang To: chemistry.-at-.ccl.net Subject: QM/MM vs. ONIOM Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, Any comments about the differences between qm/mm and oniom method are appreciated. From my point of view, they are quite similar. I hope I can get enough replies to give a summary. Thanks Zhixiang From chemistry-request@ccl.net Sun Oct 5 10:41:09 2003 Received: from mail2.qmul.ac.uk (mail2.qmul.ac.uk [138.37.6.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h95Eeb59011173 for ; Sun, 5 Oct 2003 10:40:38 -0400 Received: from smtp.qmul.ac.uk ([138.37.6.40]) by mail2.qmul.ac.uk with esmtp (Exim 4.14) id 1A6A3o-0000d5-QF for chemistry.-at-.ccl.net; Sun, 05 Oct 2003 15:40:36 +0100 Received: from tomb2.mats.qmw.ac.uk ([138.37.43.67] helo=lucylaptop) by smtp.qmul.ac.uk with smtp (Exim 3.35 #5) id 1A6A3o-00026t-00 for chemistry.-at-.ccl.net; Sun, 05 Oct 2003 15:40:36 +0100 Message-ID: <008001c38b4e$780158d0$432b258a@lucylaptop> From: "Ru-Zhen Li" To: Subject: question about the output file babel Date: Sun, 5 Oct 2003 15:39:23 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_007D_01C38B56.D9AA4990" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Sender-Host-Address: 138.37.43.67 X-QM-Scan-VirusCheck: clean X-Spam-Status: No, hits=4.7 required=7.0 tests=HTML_40_50,HTML_MESSAGE,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) This is a multi-part message in MIME format. ------=_NextPart_000_007D_01C38B56.D9AA4990 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: quoted-printable Dear all, I converted one Accelrys .car file into .pdb file with babel16, but the = output file is quite strange, it is not the same as the pdb file from = Protein Data Bank, for eg: 1. the atom name is just one character 2. the forth column of the coordinate of the atoms should be the residue = the atom belongs to, but all the name of the residue in the output file = is UNK. can anyone tell me why? thank you so much in advance!! best regards, Ru-Zhen ------=_NextPart_000_007D_01C38B56.D9AA4990 Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: quoted-printable
Dear all,
 
I converted one Accelrys .car file into = .pdb file=20 with babel16, but the output file is quite strange, it is not the same = as the=20 pdb file from Protein Data Bank, for eg:
 
1. the atom name is just one = character
2. the forth column of the coordinate = of the atoms=20 should be the residue the atom belongs to, but all the name of the = residue in=20 the output file is UNK.
 
can anyone tell me why?
 
thank you so much in = advance!!
 
best regards,
Ru-Zhen
------=_NextPart_000_007D_01C38B56.D9AA4990-- From chemistry-request@ccl.net Sun Oct 5 07:50:14 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 h95Bng59006767 for ; Sun, 5 Oct 2003 07:49:43 -0400 Received: from avdemo.tiscalinet.ch (line-0-191-bs3.tiscali.ch [212.254.0.191]) by smtp.tiscali.ch (8.11.7/8.11.7) with ESMTP id h95BnYG08180 for ; Sun, 5 Oct 2003 13:49:34 +0200 Message-Id: <5.0.2.1.0.20031005135305.00a2f7c0~at~mail.tiscalinet.ch> X-Sender: barry.hardy~at~mail.tiscalinet.ch X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Sun, 05 Oct 2003 13:53:35 +0200 To: chemistry~at~ccl.net From: Barry Hardy Subject: eCheminformatics 2003 virtual conference Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_14444853==_.ALT" X-Spam-Status: No, hits=5.2 required=7.0 tests=HTML_00_10,HTML_FONT_COLOR_BLUE,HTML_FONT_COLOR_RED, HTML_MESSAGE,MIME_LONG_LINE_QP,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) --=====================_14444853==_.ALT Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: quoted-printable Announcement and Call for Posters eCheminformatics 2003 - Virtual Conference and Poster Session To be held 10-14 Nov 2003, http://conferences.metalayer.net/echeminfo/ eCheminformatics 2003 is an international virtual conference to be held on= =20 the Internet which brings together researchers to discuss the applications= =20 of Cheminformatics methods to Drug Discovery. Please visit the=20 eCheminformatics 2003 virtual conference site=20 http://conferences.metalayer.net/echeminfo/ to sign-up and remain informed= =20 on the program. The conference will consist of live and Internet-based Virtual Lectures=20 presented through the Conference Auditorium accompanied by phone-based=20 teleconferences. Discussions with the audience will take place on the Web=20 site using both asynchronous and synchronous discussion-based mechanisms=20 and by teleconference. Archived recordings of the presentations will be=20 viewable in the Conference Library both during and after the conference. Poster Session All conference registrants have the opportunity to present a conference=20 Poster on a cheminformatics subject during the conference. Posters can be=20 presented in Word, pdf, html or Powerpoint format. If you or a colleague=20 wish to present a Poster at the conference, please submit your abstract to= =20 us with Title, author(s), institution, contact email address, contact phone= =20 number and abstract of no more than 300 words. Registrants will=20 subsequently be able to directly upload their poster to the Poster Session= =20 area of the Conference site. Speaker Presentations Web-base tools for Library Design: Tracking the Data from Conception to=20 Bio-assay & Beyond, Bradley P. Feuston, Merck Application of privileged substructure identification to drug discovery,=20 Christophe Cleva, Serono Optimized Virtual Screening, Mikl=F3s Vargyas, Chemaxon Systematic analysis of large screening sets, Paul Blower, Leadscope Extended pharmacophores in virtual screening for drug discovery, David=20 Lloyd, De Novo Pharmaceuticals Leveraging HTS Data using Drug Profiling, Andrew Lemon, ID Business=20 Solutions Ltd Quality Control in QSAR Model Development, Alex Tropsha, University of=20 North-Carolina Grid Computing on a massive scale: The University of Oxford/UD.com Screen=20 Saver Smallpox Project, Karl Harrison, Oxford University Decisions from data visualization: Cheminformatics discovery and=20 integration with other knowledge, Jeff Saffer, Omniviz Advances in Consensus Modeling for ADME/Tox Prediction, Gregory M. Banik,=20 Bio-Rad Laboratories ChemIDplus: A Free, Web-Based Portal to Compound-Based Information,=20 Mitchell Miller, Lion Bioscience Peptide to Non-Peptide: a Revolution in Virtual Screening, Mark Mackey,=20 Cresset BioMolecular Discovery Ltd High Throughput Virtual Screening, John Irwin, UCSF Sincerely, Dr. Barry Hardy Conference Secretariat barry.hardy~at~tiscalinet.ch +41 61 851 0170 --=====================_14444853==_.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Announcement and Call for Posters

eCheminformatics 2003 - Virtual Conference and Poster Session
To be held 10-14 Nov 2003, http://conferences.metalayer.net/echeminfo/

eCheminformatics 2003 is an international virtual conference to be held on the Internet which brings together researchers to discuss the applications of Cheminformatics methods to Drug Discovery.  Please visit the eCheminformatics 2003 virtual conference site h= ttp://conferences.metalayer.net/echeminfo/ to sign-up and remain informed on the program.

The conference will consist of live and Internet-based Virtual Lectures= presented through the Conference Auditorium accompanied by phone-based= teleconferences. Discussions with the audience will take place on the Web= site using both asynchronous and synchronous discussion-based mechanisms= and by teleconference. Archived recordings of the presentations will be= viewable in the Conference Library both during and after the= conference.

Poster Session

All conference registrants have the opportunity to present a conference= Poster on a cheminformatics subject during the conference. Posters can be= presented in Word, pdf, html or Powerpoint format.  If you or a= colleague wish to present a Poster at the conference, please submit your= abstract to us with Title, author(s), institution, contact email address,= contact phone number and abstract of no more than 300 words. = Registrants will subsequently be able to directly upload their poster to= the Poster Session area of the Conference site.

Speaker Presentations

Web-base tools for Library Design: Tracking the Data from Conception to= Bio-assay & Beyond, Bradley P. Feuston, Merck

Application of privileged substructure identification to drug discovery,= Christophe Cleva, Serono

Optimized Virtual Screening, Mikl=F3s Vargyas, Chemaxon

Systematic analysis of large screening sets, Paul Blower, Leadscope

Extended pharmacophores in virtual screening for drug discovery, David= Lloyd, De Novo Pharmaceuticals

Leveraging HTS Data using Drug Profiling, Andrew Lemon, ID Business= Solutions Ltd

Quality Control in QSAR Model Development, Alex Tropsha, University of= North-Carolina

Grid Computing on a massive scale: The University of Oxford/UD.com Screen= Saver Smallpox Project, Karl Harrison, Oxford University

Decisions from data visualization: Cheminformatics discovery and integration= with other knowledge, Jeff Saffer, Omniviz

Advances in Consensus Modeling for ADME/Tox Prediction, Gregory M. Banik,= Bio-Rad Laboratories

ChemIDplus: A Free, Web-Based Portal to Compound-Based Information, Mitchell= Miller, Lion Bioscience

Peptide to Non-Peptide: a Revolution in Virtual Screening, Mark Mackey,= Cresset BioMolecular Discovery Ltd

High Throughput Virtual Screening, John Irwin, UCSF


Sincerely,
Dr. Barry Hardy
Conference Secretariat
barry.hardy~at~tiscalinet.ch
+41 61 851 0170


--=====================_14444853==_.ALT-- From chemistry-request@ccl.net Sun Oct 5 11:03:05 2003 Received: from mail2.qmul.ac.uk (mail2.qmul.ac.uk [138.37.6.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h95F2Y59011761 for ; Sun, 5 Oct 2003 11:02:34 -0400 Received: from smtp.qmul.ac.uk ([138.37.6.40]) by mail2.qmul.ac.uk with esmtp (Exim 4.14) id 1A6AP3-0001iC-I2 for chemistry*at*ccl.net; Sun, 05 Oct 2003 16:02:33 +0100 Received: from tomb2.mats.qmw.ac.uk ([138.37.43.67] helo=lucylaptop) by smtp.qmul.ac.uk with smtp (Exim 3.35 #5) id 1A6AP2-0002A3-00 for chemistry*at*ccl.net; Sun, 05 Oct 2003 16:02:32 +0100 Message-ID: <019b01c38b51$88e644f0$432b258a@lucylaptop> From: "Ru-Zhen Li" To: Subject: anyone knows WHAT IF check on protein well? Date: Sun, 5 Oct 2003 16:01:20 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0198_01C38B59.EA9CF150" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Sender-Host-Address: 138.37.43.67 X-QM-Scan-VirusCheck: clean X-Spam-Status: No, hits=4.7 required=7.0 tests=HTML_40_50,HTML_MESSAGE,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) This is a multi-part message in MIME format. ------=_NextPart_000_0198_01C38B59.EA9CF150 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: quoted-printable Dear all, Now I am doing a WHAT IF check of 1n5u, and I got some results, i think = if I want to do some simulation work on the protein, I should make sure = that every serious warning or error on the check report is fixed, but = how? Thanks a lot!! Best regards, Ru-Zhen =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Ru-Zhen Li 0044 020 7882 6327 Materials Department Queen Mary University of London E1 4NS ------=_NextPart_000_0198_01C38B59.EA9CF150 Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: quoted-printable
Dear all,
 
Now I am doing a WHAT IF check of 1n5u, = and I got=20 some results, i think if I want to do some simulation work on the = protein, I=20 should make sure that every serious warning or error on the check = report is=20 fixed, but how?
 
Thanks a lot!!
 
Best regards,
Ru-Zhen
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
Ru-Zhen=20 Li
 
0044 020 7882 6327
Materials = Department
Queen=20 Mary
University of London
E1 4NS
------=_NextPart_000_0198_01C38B59.EA9CF150-- From chemistry-request@ccl.net Sun Oct 5 11:38:14 2003 Received: from kafka.net.nih.gov (mailfwd.nih.gov [165.112.130.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h95Fbf59012685 for ; Sun, 5 Oct 2003 11:37:41 -0400 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by kafka.net.nih.gov (8.12.10/8.12.9) with ESMTP id h95FbfcD019263; Sun, 5 Oct 2003 11:37:41 -0400 (EDT) Date: Sun, 5 Oct 2003 10:50:09 -0400 From: Rick Venable To: Ru-Zhen Li cc: chemistry~at~ccl.net Subject: Re: CCL:question about the output file babel In-Reply-To: <008001c38b4e$780158d0$432b258a@lucylaptop> Message-ID: References: <008001c38b4e$780158d0$432b258a@lucylaptop> ReplyTo: Rick_Venable~at~nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-1.1 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, RCVD_IN_NJABL,REFERENCES,REPLY_WITH_QUOTES,USER_AGENT_PINE, X_NJABL_OPEN_PROXY version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) I've observed the same thing for other conversions to PDB using various versions of Babel, in that most of the identifying info is lost, esp. atom and residue name. I've stopped using Babel, largely for this reason. It was easier to write a quick conversion program specific to the task at hand. On Sun, 5 Oct 2003, Ru-Zhen Li wrote: > I converted one Accelrys .car file into .pdb file with babel16, but > the output file is quite strange, it is not the same as the pdb file > from Protein Data Bank, for eg: > > 1. the atom name is just one character > 2. the forth column of the coordinate of the atoms should be the > residue the atom belongs to, but all the name of the residue in the > output file is UNK. > > can anyone tell me why? =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable~at~nih.gov ALT email: rvenable~at~speakeasy.org ------------------------------------- "Don't blame me, I voted for Kang." Homer =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=