From chemistry-request@server.ccl.net Fri Jan 12 01:11:50 2001 Received: from resstor.ndsu.nodak.edu (resstor.ndsu.NoDak.edu [134.129.111.204]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0C6Bop21831 for ; Fri, 12 Jan 2001 01:11:50 -0500 Received: from hotmail.com (sud8b.pharm.ndsu.NoDak.edu [134.129.118.52]) by resstor.ndsu.nodak.edu (8.9.3/8.9.3) with ESMTP id AAA24499; Fri, 12 Jan 2001 00:11:50 -0600 Message-ID: <3A5E9C27.368CEB0C@hotmail.com> Date: Thu, 11 Jan 2001 23:54:48 -0600 From: xin_hu Organization: NDSU X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net CC: CHEMISTRY@ccl.net Subject: Re: CCL:basis set optimiser in solid References: <3A5CE2B9.B09726E1@mcmaster.ca> Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 7bit Hello: I am a newer of AMBER6.0 and just try to learn how to use it. Maybe it is a stupid question but hopefully someone give me a help. My questions are 1) Can I load a pdb file of protein, assign the residues with charges, and save the file as pdb or other type formate? if can, what's kind of charge it is assigned? 2) How to just add polar hydrogen (united atom) to residues, and how to assign the kollman united atom charges using AMBER6.0? I appreciate your help. Thanks. xin hu Dept of Pharmacy NDSU Samantha Jenkins wrote: > Sergei Tretiak wrote: > > > > Kevin, > > > > MOLDEN (http://www.cmbi.kun.nl/~schaft/molden/molden.html) will do the > > job for you. It can generate graphics GIF files for each step and play it > > like a movie, but to merge all GIFs into a single movie file you have to > > use another software. > > > > Best, > > > > Sergei > > > > >.-----------------------------------------------------------------------. > > |\ / \ | Sergei Tretiak | / \ /| > > |.\/...\|.......................................................|/...\/.| > > | Theoretical Division | Voice: (505) 667-8351 | > > | Mail stop B262 | Fax: (505) 665-4063 | > > | Los Alamos National Lab | E-mail: serg@markov.chem.rochester.edu | > > | Los Alamos, NM 87545 | serg@wigner.chem.rochester.edu | > > | Homepage: http://markov.chem.rochester.edu/serg/welcome.html | > > |_______________________________________________________________________| > Hello. > > I am trying to optimise basis sets using LOPTCG within crytsal98 and I > am having little success. Does anyone have a working set of input files > for LOPTCG, which optimse the basis set. The code seem to work OK for > geometries and comes with example files for the geometries, but not the > basis sets. > Any simple solid would do, diamond etc. > > Thanks, > > Samantha Jenkins > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- ************************************************* Xin Hu Department of Pharmaceutical Science College of Pharmacy North Dakota State University Fargo, ND 58105 Tel: 701-231-8298 (O) 701-231-4360 (H) Fax: 701-231-7781 E-mail: Xin_Hu@ndsu.nodak.edu xxh0541@hotmail.com ************************************************* From chemistry-request@server.ccl.net Fri Jan 12 06:22:17 2001 Received: from mail-b.bcc.ac.uk (mail-b.bcc.ac.uk [144.82.100.22]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0CBMGp22320 for ; Fri, 12 Jan 2001 06:22:16 -0500 Received: from dale.ri.ac.uk by mail-b.bcc.ac.uk with SMTP (Mailer) with ESMTP; Fri, 12 Jan 2001 11:22:03 +0000 Received: from ri.ac.uk (davy.ri.ac.uk) by dale.ri.ac.uk (Content Technologies SMTPRS 4.1.5) with SMTP id for ; Fri, 12 Jan 2001 11:18:43 +0000 Received: from tyndall.ri.ac.uk by ri.ac.uk (5.x/SMI-SVR4) id AA04334; Fri, 12 Jan 2001 11:22:01 GMT Received: from localhost by tyndall.ri.ac.uk (980427.SGI.8.8.8) id LAA98544; Fri, 12 Jan 2001 11:22:01 GMT Date: Fri, 12 Jan 2001 11:22:00 +0000 From: "DFT on Complex Oxides; Workshop/School at the DFRL, 2001" X-Sender: dft@tyndall To: chemistry@ccl.net Subject: Call for papers: DFT for Complex Oxides - London (UK) 14-18/05/2001 Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Colleagues, we would like to announce that the programme and call for papers for the school and workshop "Density Functional Theory for the Study of Complex Oxides" have now been published, and are available at the following address: http://www.ri.ac.uk/DFT2001 This event will take place at the Royal Institution of Great Britain, in central London (UK), the 14-18 May 2001. Registration is now open. Applications for oral contributions should be received by February 2nd 2001, while the deadline for registration at standard fees is March 18th 2001. If you would like to receive further information, you can contact the organisers at dft@ri.ac.uk We look forward to hearing from you. Yours sincerely, the local organising committee =============================================================================== Density Functional Theory for the Study of Complex Oxides The Royal Institution of Great Britain, London, 14-18 May 2001 Organising Committee: M. Alfredsson, F. Cora' and A.A. Sokol (Davy-Faraday Research Laboratory, The Royal Institution of Great Britain, 21 Albemarle Street, London W1X 4BS - UK) J.D. Gale (Dept. of Chemistry, Imperial College, Exhibition Road, London SW7 2AY - UK) N.M. Harrison (CCLRC - Daresbury Laboratory, Daresbury, Warrington, WA4 4AD - UK) e-mail: dft@ri.ac.uk Tel. + 44 - 207 - 4092992 Fax. + 44 - 207 - 6293569 Conference web site: http://www.ri.ac.uk/DFT2001 =============================================================================== ********************************************************************** This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you have received this email in error please notify the system manager. This footnote also confirms that this email message has been swept by MIMEsweeper for the presence of computer viruses. www.mimesweeper.com ********************************************************************** From chemistry-request@server.ccl.net Fri Jan 12 09:58:39 2001 Received: from power.curtin.edu.au ([134.7.118.91]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0CEwbp23432 for ; Fri, 12 Jan 2001 09:58:37 -0500 Received: from [192.168.50.100] ([130.95.222.52]) by power.curtin.edu.au (8.10.2/8.10.2/SuSE Linux 8.10.0-0.3) with ESMTP id f0CF1vV12731 for ; Fri, 12 Jan 2001 23:01:59 +0800 X-Authentication-Warning: power.curtin.edu.au: Host [130.95.222.52] claimed to be [192.168.50.100] Mime-Version: 1.0 X-Sender: andrew@power.curtin.edu.au (Unverified) Message-Id: Date: Fri, 12 Jan 2001 22:11:03 +0800 To: CHEMISTRY@ccl.net From: Andrew Rohl Subject: rasmol for OS X? Content-Type: text/plain; charset="us-ascii" ; format="flowed" Has anyone carbonized RasMol for the Mac, so it runs natively on Mac OS X? I should be writing papers etc but am thinking of doing the porting if noone else has... Andrew -- ------------------------------------------------------------------------------ Andrew Rohl Email: A.Rohl@curtin.edu.au Senior Lecturer in Computational Chemistry School of Applied Chemistry Phone: +61 8 9266 7317 (Office) Curtin University of Technology +61 8 9266 3780 (Lab) PO Box U 1987 Perth, 6845 FAX: +61 8 9266 2300 WESTERN AUSTRALIA WWW: http://chemistry.curtin.edu.au/staff/alr ------------------------------------------------------------------------------ From chemistry-request@server.ccl.net Fri Jan 12 09:58:26 2001 Received: from power.curtin.edu.au (power.curtin.edu.au [134.7.118.91]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0CEwNp23421 for ; Fri, 12 Jan 2001 09:58:23 -0500 Received: from [192.168.50.100] ([130.95.222.52]) by power.curtin.edu.au (8.10.2/8.10.2/SuSE Linux 8.10.0-0.3) with ESMTP id f0CF20V12734 for ; Fri, 12 Jan 2001 23:02:00 +0800 X-Authentication-Warning: power.curtin.edu.au: Host [130.95.222.52] claimed to be [192.168.50.100] Mime-Version: 1.0 X-Sender: andrew@power.curtin.edu.au (Unverified) Message-Id: Date: Fri, 12 Jan 2001 22:55:53 +0800 To: CHEMISTRY@ccl.net From: Andrew Rohl Subject: fast bond render Content-Type: multipart/mixed; boundary="============_-1232811129==_============" --============_-1232811129==_============ Content-Type: text/plain; charset="us-ascii" ; format="flowed" I am writing (yet another) java applet for displaying and allowing rotation of molecules in a web page. Of the free applets out there, i have not found one which displays ball and stick representations to my satisfaction. As the applet is to be used in a first year undergraduate virtual lab, i think that a good ball and stick representation is vitally important and the applet I produce will be freeware. I have started with an applet written by Eric Harlow (brain@netbrain.com) and shamelessly used the atom style in the program Ball&Stick by Norbert Mueller and coworkers. The results can be seen in the attached (small!) picture. The applet is the top and the ball & stick at the bottom. Now my question relates to the best way of drawing realistic bonds as in the bottom figure. Dr Mueller has been very kind in telling me how Ball & Stick draws the bonds but I suspect using his method will lead to the applet no longer having satisfactory performance. So does anyone have any algorithms or code fragments for the fast rendering of bonds? I am aware of the JMol code, but its bonds appear to be ribbons, rather than cylinders and so this code loses its 3-Dness. 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http://chemistry.curtin.edu.au/staff/alr ------------------------------------------------------------------------------ --============_-1232811129==_============-- From chemistry-request@server.ccl.net Fri Jan 12 11:09:18 2001 Received: from resstor.ndsu.nodak.edu (resstor.ndsu.NoDak.edu [134.129.111.204]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0CG9Ip24051 for ; Fri, 12 Jan 2001 11:09:18 -0500 Received: from hotmail.com (sud8b.pharm.ndsu.NoDak.edu [134.129.118.52]) by resstor.ndsu.nodak.edu (8.9.3/8.9.3) with ESMTP id KAA32618; Fri, 12 Jan 2001 10:09:18 -0600 Message-ID: <3A5F27BF.5678BB28@hotmail.com> Date: Fri, 12 Jan 2001 09:50:24 -0600 From: xin_hu Organization: NDSU X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: AMBER6.0 HELP References: <3A5CE2B9.B09726E1@mcmaster.ca> <3A5E9C27.368CEB0C@hotmail.com> Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 7bit Hello: I am a newer of AMBER6.0 and just try to learn how to use it. Maybe it is a stupid question but hopefully someone give me a help. My questions are 1) Can I load a pdb file of protein, assign the residues with charges, and save the file as pdb or other type formate? if can, what's kind of charge it is assigned? 2) How to just add polar hydrogen (united atom) to residues, and how to assign the kollman united atom charges using AMBER6.0? I appreciate your help. Thanks. xin hu > > -- > ************************************************* > Xin Hu > Department of Pharmaceutical Science > College of Pharmacy > North Dakota State University > Fargo, ND 58105 > Tel: 701-231-8298 (O) > 701-231-4360 (H) > Fax: 701-231-7781 > E-mail: Xin_Hu@ndsu.nodak.edu > xxh0541@hotmail.com > ************************************************* > -- ************************************************* Xin Hu Department of Pharmaceutical Science College of Pharmacy North Dakota State University Fargo, ND 58105 Tel: 701-231-8298 (O) 701-231-4360 (H) Fax: 701-231-7781 E-mail: Xin_Hu@ndsu.nodak.edu xxh0541@hotmail.com ************************************************* From chemistry-request@server.ccl.net Fri Jan 12 12:09:26 2001 Received: from relay1.scripps.edu (relay1.scripps.edu [137.131.200.29]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0CH9Qp24600 for ; Fri, 12 Jan 2001 12:09:26 -0500 Received: from gamow.scripps.edu (gamow.scripps.edu [137.131.252.67]) by relay1.scripps.edu (8.11.0/TSRI-4.0r) with ESMTP id f0CH7P425523; Fri, 12 Jan 2001 09:07:25 -0800 (PST) Received: (from case@localhost) by gamow.scripps.edu (8.9.1a/TSRI-2.8) id JAA157211; Fri, 12 Jan 2001 09:07:25 -0800 (PST) Date: Fri, 12 Jan 2001 09:07:25 -0800 From: David Case To: xin_hu Cc: CHEMISTRY@ccl.net Subject: Re: CCL:basis set optimiser in solid Message-ID: <20010112090725.A156683@gamow.scripps.edu> References: <3A5CE2B9.B09726E1@mcmaster.ca> <3A5E9C27.368CEB0C@hotmail.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i In-Reply-To: <3A5E9C27.368CEB0C@hotmail.com>; from xxh0541@hotmail.com on Thu, Jan 11, 2001 at 11:54:48PM -0600 On Thu, Jan 11, 2001, xin_hu wrote: > Can I > load a pdb file of protein, assign the residues with charges, > and save the file as pdb or other type formate? if can, what's > kind of charge it is assigned? The standard libraries have alternate charge states (protonated and unprotonated) for his, glu and asp. You could make others and add to the library, or manually modify charges using a spread-sheet like interface. The file can be saved as PDB or Amber format. All of this is done in LEaP, which has an on-line manual, a printed Users' Guide and a tutorial section. > How to just add polar hydrogen (united atom) to residues, and how to > assign the kollman united atom charges using AMBER6.0? Run xleap -s (to ignore the default startup file), then type "source leaprc.ff91". This will load in the "parm91" (Weiner et al. united atom force field). Because this force field is so old (developed in 1983-84) it is not used much anymore; be sure this is what you really want before spending a lot of time at it. Amber6 is really designed with more recent force fields in mind. ...good luck...dac -- ================================================================== David A. Case | e-mail: case@scripps.edu Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | http://www.scripps.edu/case ================================================================== From chemistry-request@server.ccl.net Fri Jan 12 13:44:51 2001 Received: from relay2.scripps.edu (relay2.scripps.edu [137.131.200.30]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f0CIiop24775 for ; Fri, 12 Jan 2001 13:44:51 -0500 Received: from gamow.scripps.edu (gamow.scripps.edu [137.131.252.67]) by relay2.scripps.edu (8.11.0/TSRI-4.0r) with ESMTP id f0CIgna17990; Fri, 12 Jan 2001 10:42:49 -0800 (PST) Received: (from case@localhost) by gamow.scripps.edu (8.9.1a/TSRI-2.8) id KAA157735; Fri, 12 Jan 2001 10:42:49 -0800 (PST) Date: Fri, 12 Jan 2001 10:42:49 -0800 From: David Case To: CHEMISTRY@ccl.net Cc: xxh0541@hotmail.com Subject: Re: CCL: united atom force fields in Amber Message-ID: <20010112104249.B157584@gamow.scripps.edu> References: <3A5CE2B9.B09726E1@mcmaster.ca> <3A5E9C27.368CEB0C@hotmail.com> <20010112090725.A156683@gamow.scripps.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.2.5i In-Reply-To: <20010112090725.A156683@gamow.scripps.edu>; from case@scripps.edu on Fri, Jan 12, 2001 at 09:07:25AM -0800 On Fri, Jan 12, 2001, David Case wrote: > > > How to just add polar hydrogen (united atom) to residues, and how to > > assign the kollman united atom charges using AMBER6.0? > > Run xleap -s (to ignore the default startup file), then type > "source leaprc.ff91". This will load in the "parm91" (Weiner et al. united > atom force field). Because this force field is so old (developed in > 1983-84) it is not used much anymore; be sure this is what you really want > before spending a lot of time at it. Amber6 is really designed with more > recent force fields in mind. .ooops...this answer was incorrect. A more complex procedure is needed to really get the original 1984 polar-hydrogen-only force field. The procedure mentioned above actually gets the all-atom 1986 force field. (They are both called Weiner et al....) My apologies for any confusion this has caused. ...dac -- ================================================================== David A. Case | e-mail: case@scripps.edu Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | http://www.scripps.edu/case ==================================================================