From chemistry-request@server.ccl.net Thu Aug 23 00:21:58 2001 Received: from baton.phys.lsu.edu ([130.39.182.71]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7N4LwM05569 for ; Thu, 23 Aug 2001 00:21:58 -0400 Received: (from vani@localhost) by baton.phys.lsu.edu (8.9.2/8.9.2) id XAA03352; Wed, 22 Aug 2001 23:18:47 -0500 (CDT) Date: Wed, 22 Aug 2001 23:18:46 -0500 (CDT) From: Vemparala Satyavani To: chemistry@ccl.net Subject: residue change in AMBER Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Is there a way to change a residue in a protein and then do energy minimisations and run MD on the new structure in AMBER?..(with our knowing apriori the positions of the new residue).. i.e., if a protein has a sequence : GLN PRO ASN TRP ASN..and i want to see what happens if i change TRP to say GLN.. can i do that in AMBER? Thanks vani From chemistry-request@server.ccl.net Thu Aug 23 05:21:23 2001 Received: from arrhenius.che.chalmers.se ([129.16.90.200]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7N9LMM19953 for ; Thu, 23 Aug 2001 05:21:22 -0400 Received: from [129.16.96.114] (rubidium.oc.chalmers.se [129.16.96.114]) by arrhenius.che.chalmers.se (8.9.3/8.9.3) with ESMTP id LAA1107311 for ; Thu, 23 Aug 2001 11:21:34 +0200 (MDT) Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 23 Aug 2001 11:21:18 +0200 To: chemistry@ccl.net From: Peter =?iso-8859-1?Q?Din=E9r?= Subject: AMD vs Pentium for G98 calc. in Linux? Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f7N9LNM19966 Dear CCL subscribers, (Sorry if you have heard similar questions before, but I can´t access the the search function in the CCL archives at the moment) We are going to set up some workstation to do G98 (linux redhat) calculations. Do tou have any recommendations to what processor that has the best performance (AMD, PIII, or P4) for this kind of calculation. I would be greatful if I can get some advice or www-adresses with benchmark calculations. (if you e-mail me directly we don´t have to too many answers on the list, instead I will summarize) /peter dinér .-------------------------------------------------------------------. | Ph. D. Student | \\/|\|/ | Department of Chemistry | | Peter Dinér | / o o \ | Organic Chemistry | | Mail: diner@organic.gu.se | G O G | Göteborg University | | Phone: +46-31-772 2901 | \ \_/ / | Kemivägen 10 | | Fax: +46-31-772 3840 | \___/ | S-412 96 Göteborg | | | | Sweden | .-------------------------------------------------------------------. From chemistry-request@server.ccl.net Thu Aug 23 01:01:22 2001 Received: from deakin.edu.au (root@[128.184.136.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7N51KM06226 for ; Thu, 23 Aug 2001 01:01:21 -0400 Received: from [128.184.88.189] (128-184-88-189.bcs.deakin.edu.au [128.184.88.189]) by deakin.edu.au (8.11.4/8.11.4) with ESMTP id f7N50sW01411; Thu, 23 Aug 2001 15:00:54 +1000 (EST) Mime-Version: 1.0 X-Sender: lim@128.184.136.2 Message-Id: Date: Thu, 23 Aug 2001 15:03:19 +1000 To: Recipient List Suppressed:; From: "Kieran F Lim (Lim Pak Kwan)" Subject: Chime is incompatible with latest Microsoft Internet Explorer Content-Type: text/plain; charset="us-ascii" ; format="flowed" Hello everyone, Netscape Chime and Chime Pro are very useful chemistry web-browser plug-ins. I just got this information from the MDL Information web site http://www.mdli.com/cgi/dynamic/welcome.html Kieran ============================================ Microsoft IE 5.5 SP2 Does Not Support Chime and Chime Pro August 3, 2001 Dear Chime and Chime Pro users: MDL has learned that a new service pack of the Microsoft Internet Explorer browser (5.5 SP2) has been released today without support for the Netscape plug-in interface used by Chime and Chime Pro. Our understanding is that future versions of Microsoft Internet Explorer will also lack this interface. This would mean that the Chime and Chime Pro plug-ins would not be supported on these new versions of Microsoft Internet Explorer (including 6.0) until further notice. This issue does not affect the Netscape Communicator 4.7 browser. MDL is working closely with Microsoft to evaluate alternatives for supporting Chime and Chime Pro with new versions of Internet Explorer. Until further notice, Chime and Chime Pro users should continue to use older versions of Internet Explorer (5.5 SP1 and lower) or Netscape Communicator 4.7, which are supported with Chime and Chime Pro 2.6 SP2. MDL will post updates to this information and the Hardware and Software requirements on its MDL Chime site at the following URL: http://www.mdlchime.com/chime Thank you for your patience and understanding while we address these issues. Regards, MDL Chime Product Management ------------------------------------------------------------ Dr Kieran F Lim Biol. and Chemical Sciences (Lim Pak Kwan) Deakin University ph: + [61] (3) 5227-2146 Geelong VIC 3217 fax: + [61] (3) 5227-1040 AUSTRALIA mailto:lim@deakin.edu.au http://www.deakin.edu.au/~lim From chemistry-request@server.ccl.net Thu Aug 23 09:18:14 2001 Received: from shiva.jussieu.fr ([134.157.0.129]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7NDIDM28292 for ; Thu, 23 Aug 2001 09:18:13 -0400 Received: from liliput.lct.jussieu.fr (liliput.lct.jussieu.fr [134.157.90.1]) by shiva.jussieu.fr (8.11.3/jtpda-5.3.3) with ESMTP id f7NDICO79367 for ; Thu, 23 Aug 2001 15:18:13 +0200 (CEST) Received: from (pollet@localhost) by liliput.lct.jussieu.fr (8.10.1/jtpda-5.3.3) id f7NDIH229318 for chemistry@ccl.net; Thu, 23 Aug 2001 15:18:17 +0200 (FRA Ete) From: rodolphe.pollet@lct.jussieu.fr (Rodolphe Pollet) Message-Id: <200108231318.f7NDIH229318@liliput.lct.jussieu.fr> Subject: ab initio methods To: chemistry@ccl.net Date: Thu, 23 Aug 2001 15:18:16 +0200 (FRA Ete) X-Mailer: ELM [version 2.4ME+ PL66 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CCL'ers, I am looking for a single reference, such as a review article or a book, about the ab initio methods MRCI, CASPT2, AQCC, ... These ones are indeed not covered in the Szabo&Ostlund book. Thanks very much in advance Rodolphe Pollet From chemistry-request@server.ccl.net Thu Aug 23 13:04:46 2001 Received: from phm.utoronto.ca ([128.100.70.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7NH4kM02416 for ; Thu, 23 Aug 2001 13:04:46 -0400 Received: from phm.utoronto.ca (lpk04.phm.utoronto.ca [128.100.70.180]) by phm.utoronto.ca (8.9.3+Sun/8.9.3) with ESMTP id MAA15447; Thu, 23 Aug 2001 12:58:35 -0400 (EDT) Sender: william@phm.utoronto.ca Message-ID: <3B85371E.8B0194CA@phm.utoronto.ca> Date: Thu, 23 Aug 2001 13:02:22 -0400 From: William Wei Reply-To: william@phm.utoronto.ca Organization: Faculty of Pharmacy, U of T X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: David Konerding , hoofnagl@SDSC.EDU, dek@cgl.ucsf.EDU, strahan@outerbanks.umaryland.edu, noronha@dedalus.lcc.ufmg.br, case@scripps.edu, CHEMISTRY@ccl.net Subject: Re: CCL:About amber parameters References: <200108202029.NAA230304@socrates.cgl.ucsf.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Dear CCLers, I posted my problem of developing amber parameters with my inhibitor two days ago. I got much help from Andy, David Konerding, Gary, antonio luiz oliveira de noronha, and David Case. Thank you very much. I reconstructure my inhibitor in Xleap, and modified the parameters. Now it runs well. My previous mistake was I have changed the residue name in .OFF file. For I want to use my residue name. For example, I have imported residues from amber, after I saved to .OFF file, in my pdb file, there were the amber residue name in it. If I want to change all the residue name to mine, Can I do that? Or can anyone give me the information of .OFF file format? Thanks in advance. William. From chemistry-request@server.ccl.net Thu Aug 23 09:47:20 2001 Received: from schrodinger.com (root@[192.156.98.99]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7NDlKM28968 for ; Thu, 23 Aug 2001 09:47:20 -0400 Received: from mirabelle.schrodinger.com (mirabelle.schrodinger.com [216.216.237.102]) by schrodinger.com (8.8.5/8.8.5) with ESMTP id GAA03491; Thu, 23 Aug 2001 06:47:18 -0700 Received: from localhost (shenkin@localhost) by mirabelle.schrodinger.com (8.9.3/8.8.5) with ESMTP id JAA17934; Thu, 23 Aug 2001 09:45:55 -0400 X-Authentication-Warning: mirabelle.schrodinger.com: shenkin owned process doing -bs Date: Thu, 23 Aug 2001 09:45:55 -0400 (EDT) From: Peter Shenkin To: cc: Subject: Re: CCL:Superimpose/Superposition cyclic peptides In-Reply-To: <200108151753.TAA99443@xaver.org.chemie.tu-muenchen.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, XCluster, which is part of the MacroModel package, can come close, provided the backbone atoms you wish to superimpose are actually cyclic. For instance, suppose you were superimposing just CA's of a pentapeptide and the CA's have atom numbers 1, 4, 7, 10, 13. The program (if told to observe cyclic symmetry), would compare each pair of conformations 10 ways, picking the lowest RMS as the value it would use in the clustering. If conf 1 has the atoms in the above order, conf 2 would be compared in the following registrations with conf 1: 1 4 7 10 13 4 7 10 13 1 1 10 13 1 4 ... (2 more like this) 1 13 10 7 4 13 10 7 4 1 10 7 4 1 13 ... (2 more like this) The problem is that you probably don't want the second 5 ways. The next version of the program (due out in Oct or Nov of this year) will have automatic symmetry detection, and would do all this automatically, including keeping just the comparisons consistent with the overall symmetry of the system. Obviously, you do want to compare things in both directions if the ring atoms look the same going around in both directions, as in cyclohexane. You can learn more about how it's done now by going to our web site, then support, then on-line manuals, then XCluster. Hope this helps, -P. On Wed, 15 Aug 2001 Robert.Guenther@ch.tum.de wrote: > Dear CCL'ers, > > starting a new project on the conformational properties cyclic penta- > and hexapeptides the following problem came up: > I have about 50 different cyclopeptides with a known 3-dimensional conformation > (either determined by experiments or obtained by strucutural calculation using > molecular dynamics). My goal is to take these structures, cluster their backbone > conformations and derive some conformational families. > Unfortunately, the residue numbering within the cyclic peptides is somehow > arbitary, thus preventing a simple atom-on-atom superimposing, e.g. the molecule > cyclo-(Pro-Ala-Ala-Ala-Ala) could have the same conformation as cyclo-(Ala-Ala- > Pro-Ala-Ala) but it is not detected by common superimposing fomralisms, because > the numbering scheme of the residues is different (the Pro's have the number 1 > and 3 respectively). > Does anyone knows about a programm or formalism which could help me to tackle > this problem? Any hint is appreciated and will be posted on CCL. > > Thanx in advance, > Robert > > +---------------------------------------------------------------+ > | Dr. Robert Guenther [e-mail:Robert.Guenther(at)ch.tum.de] |-+ > | Institut fuer organische Chemie und Biochemie II, TU Muenchen |#| > | Lichtenbergstr. 4, D-85747 Garching |#| > +---------------------------------------------------------------+#| > +----------------------------------------------------------------+ > > > > -= 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 > > > > > -- Peter S. Shenkin Schrodinger, Inc. VP, Software Development 120 W. 45th St. 646 366 9555 x111 Tel New York, NY 10036 646 366 9550 FAX shenkin@schrodinger.com http://www.schrodinger.com From chemistry-request@server.ccl.net Thu Aug 23 12:27:10 2001 Received: from gallium.chem.vu.nl ([130.37.144.37]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7NGRAM32135 for ; Thu, 23 Aug 2001 12:27:10 -0400 Received: from chem.vu.nl (far15.chem.vu.nl [130.37.148.80]) by gallium.chem.vu.nl (8.9.1a/8.9.1) with ESMTP id SAA75024 for ; Thu, 23 Aug 2001 18:27:09 +0200 Sender: jongejan@chem.vu.nl Message-ID: <3B852ECE.BB0F59E1@chem.vu.nl> Date: Thu, 23 Aug 2001 18:26:54 +0200 From: Aldo Jongejan X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Povscript Content-Type: multipart/alternative; boundary="------------96BAC1F8B6A92B0A278B4DFF" --------------96BAC1F8B6A92B0A278B4DFF Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, I am trying to get a copy of Povscript, an "extension" to Molscript written by Daniel Peisach. I can't reach Dr. Peisach's server, so if anybody could help me to a copy of his program or has some information about it, please send me an e-mail. with kind regards, aldo -- ########################################### Aldo Jongejan Molecular Modeling Group Dept. of Pharmacochemistry Free University of Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands e-mail: jongejan@chem.vu.nl tlf: +31 (0)20 4447612 fax: +31 (0)20 4447610 ########################################### --------------96BAC1F8B6A92B0A278B4DFF Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all,

I am trying to get a copy of Povscript, an "extension" to Molscript
written by Daniel Peisach. I can't reach Dr. Peisach's server, so
if anybody could help me to a copy of his program or has some
information about it, please send me an e-mail.

with kind regards,

aldo 

-- 
###########################################

Aldo Jongejan
Molecular Modeling Group
Dept. of Pharmacochemistry
Free University of Amsterdam
De Boelelaan 1083
1081 HV Amsterdam
The Netherlands

e-mail: jongejan@chem.vu.nl
tlf:    +31 (0)20 4447612
fax:    +31 (0)20 4447610

###########################################
  --------------96BAC1F8B6A92B0A278B4DFF-- From chemistry-request@server.ccl.net Thu Aug 23 15:46:30 2001 Received: from dylan.cse.nd.edu ([129.74.32.170]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7NJkUM09039 for ; Thu, 23 Aug 2001 15:46:30 -0400 Received: from localhost (ako@localhost) by dylan.cse.nd.edu (8.10.2/8.10.2) with ESMTP id f7NJkSr10156 for ; Thu, 23 Aug 2001 14:46:28 -0500 (EST) Date: Thu, 23 Aug 2001 14:46:28 -0500 (EST) From: Alice NgarKit Ko To: chemistry@ccl.net Subject: moving molecules Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, Does anyone know how to move molecules around? I want to move some water molecules in some specific area inside my protein. But I don't know the xyz coordinates of the target locations. I would like to be able to visualize the protein and the water molecules, and then just use the mouse to drag the water molecules into my protein. Is there any software out there can do that? I would appreciate any suggestion. Thank you very much Alice From chemistry-request@server.ccl.net Thu Aug 23 17:30:29 2001 Received: from ks.uiuc.edu ([130.126.120.73]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7NLUTM12976 for ; Thu, 23 Aug 2001 17:30:29 -0400 Received: from glasgow.ks.uiuc.edu (glasgow.ks.uiuc.edu [130.126.120.45]) by ks.uiuc.edu (8.11.2/8.11.2) with ESMTP id f7NLUSr01311; Thu, 23 Aug 2001 16:30:28 -0500 (CDT) Received: (from barryi@localhost) by glasgow.ks.uiuc.edu (8.9.3+Sun/8.9.1) id QAA25557; Thu, 23 Aug 2001 16:30:28 -0500 (CDT) Date: Thu, 23 Aug 2001 16:30:28 -0500 From: Barry Isralewitz To: Alice NgarKit Ko Cc: chemistry@ccl.net Subject: Re: CCL:moving molecules Message-ID: <20010823163021.A25499@glasgow.ks.uiuc.edu> Mail-Followup-To: Barry Isralewitz , Alice NgarKit Ko , chemistry@ccl.net References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.3.7i In-Reply-To: ; from ako@cse.nd.edu on Thu, Aug 23, 2001 at 02:46:28PM -0500 Hi, On Thu, Aug 23, 2001 at 02:46:28PM -0500, Alice NgarKit Ko wrote: > Hi all, > > Does anyone know how to move molecules around? I want to move some water > molecules in some specific area inside my protein. But I don't know the > xyz coordinates of the target locations. I would like to be able to > visualize the protein and the water molecules, and then just use the mouse > to drag the water molecules into my protein. Is there any software out > there can do that? I would appreciate any suggestion. > Thank you very much > > Alice The molecular visualization program VMD offers a couple of ways to do this. You can simply move static molecules, or get as fancy as real-time interactive force-feedback molecular dynamics (when connected to the parallel MD program NAMD). VMD is released by the Theoretical Biophysics Group, at the University of Illinois at Urbana-Champaign. VMD is free academic software, download it at: http://www.ks.uiuc.edu/Research/vmd/ The easiest way to move molecules is described in the online documentation for VMD, see "Move Mode" in the "Mouse Form: Object Menus" section. After the move, just write out the new coordinates to a .pdb file. http://www.ks.uiuc.edu/Research/vmd/current/ug/node36.html#SECTION00742400000000000000 (Obligatory bias admission: I do some programming for VMD nowadays.) Happy modeling, Barry -- Barry Isralewitz Beckman 3121 Theoretical Biophysics Group, UIUC Office Phone: (217) 244-1612 Home Phone: (217) 337-6364 email: barryi@ks.uiuc.edu http://www.ks.uiuc.edu/~barryi From chemistry-request@server.ccl.net Thu Aug 23 20:04:30 2001 Received: from mercury.sunesis.com ([64.240.200.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7O04QM18545 for ; Thu, 23 Aug 2001 20:04:26 -0400 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: RE: moving molecules X-MimeOLE: Produced By Microsoft Exchange V6.0.4712.0 Date: Thu, 23 Aug 2001 17:01:45 -0700 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: moving molecules Thread-Index: AcEsDFjxf9uo00AYSCWCqzV6L5YHcAAIqT1w From: "DeLano, Warren" To: "Alice NgarKit Ko" , Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f7O04UM18546 This is a trivial task in PyMOL, which is free and open-source. http://pymol.sourceforge.net 1. Load structure as a PDB file (File Menu). 2. Put mouse into editing mode (Mouse Menu). 3. Control-middle-click on water you want to move (a spherical baton will appear). 4. Then shift-middle-click on the baton to drag the water around. 5. Save modified PDB file (File Menu). Cheers, Warren -- mailto:warren@sunesis.com Warren L. DeLano, Ph.D. Informatics Scientist Sunesis Pharmaceuticals, Inc. 341 Oyster Point Blvd. S. San Francisco, CA 94080 (650)-266-3606 fax: (650)-266-3501 > -----Original Message----- > From: Alice NgarKit Ko [mailto:ako@cse.nd.edu] > Sent: Thursday, August 23, 2001 12:46 PM > To: chemistry@ccl.net > Subject: CCL:moving molecules > > > Hi all, > > Does anyone know how to move molecules around? I want to > move some water > molecules in some specific area inside my protein. But I > don't know the > xyz coordinates of the target locations. I would like to be able to > visualize the protein and the water molecules, and then just > use the mouse > to drag the water molecules into my protein. Is there any > software out > there can do that? I would appreciate any suggestion. > > Thank you very much > > Alice > > > -= 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 > > > > > >