From chemistry-request@ccl.net Sun Sep 14 23:51:13 2003 Received: from mercury.chem.pitt.edu (mercury.chem.pitt.edu [136.142.60.100]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8F3ogBS031002 for ; Sun, 14 Sep 2003 23:50:42 -0400 Received: from ringo.chem.pitt.edu (localhost.localdomain [127.0.0.1]) by mercury.chem.pitt.edu (Postfix) with SMTP id 04F15484F for ; Sun, 14 Sep 2003 23:26:34 -0400 (EDT) Received: from 200.165.141.192 (SquirrelMail authenticated user gustavo) by mercury.chem.pitt.edu with HTTP; Sun, 14 Sep 2003 23:26:34 -0400 (EDT) Message-ID: <2497.200.165.141.192.1063596394.squirrel(at)mercury.chem.pitt.edu> Date: Sun, 14 Sep 2003 23:26:34 -0400 (EDT) Subject: INDO/S with double excitations From: To: X-Priority: 3 Importance: Normal X-Mailer: SquirrelMail (version 1.2.11) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=0.8 required=7.0 tests=NO_REAL_NAME version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCL readers, I have been reading papers dealing with the Sum Over States (SOS) calculation of two-photon absorption cross sections of organic molecules with the INDO/S methodology. In these papers the authors include single and double excitations in the CI. As far as I know, the INDO/S methodology was parameterized for single excitations only. The authors of these papers don't say why they need to include double excitations in the calculations. Does someone on this list know the reason for including these double excitations in these INDO/S calculations? Thank you very much in advance. I will summarize. Sincerely yours, Gustavo L.C. Moura gustavo(at)mercury.chem.pitt.edu From chemistry-request@ccl.net Mon Sep 15 09:32:05 2003 Received: from yangtze.hku.hk (yangtze.hku.hk [147.8.148.244]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8FDVWBS032356 for ; Mon, 15 Sep 2003 09:31:33 -0400 Received: from localhost (martin@localhost) by yangtze.hku.hk (8.11.6/8.9.3) with ESMTP id h8F6tk013842 for ; Mon, 15 Sep 2003 14:55:46 +0800 Date: Mon, 15 Sep 2003 14:55:46 +0800 (HKT) From: Ma Chi Chiu To: CHEMISTRY:at:ccl.net Subject: Question about CHARMM 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) Dear all, I am trying to perform MD simulation with CHARMM and I got two problems as below: 1. How to set up initial velocity to each atom before the simulation? 2. How to read the binary dcd file? Thank you very much Martin From chemistry-request@ccl.net Mon Sep 15 09:30:21 2003 Received: from mail.fescomail.net ([202.94.7.253]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h8FDTbBS032227 for ; Mon, 15 Sep 2003 09:29:40 -0400 Received: (qmail 6462 invoked by uid 2000); 15 Sep 2003 21:30:46 -0000 Message-ID: <20030915213046.6461.qmail/at/mail.fescomail.net> From: "xiongying99" To: chemistry/at/server.ccl.net Subject: the probelm for =?gb2312?Q?=22pdbqtopdb=22?= command in Autodock Date: Mon, 15 Sep 2003 21:30:45 +0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed; charset="gb2312" Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=3.7 required=7.0 tests=DEAR_SOMETHING,FROM_ENDS_IN_NUMS,MAILTO_TO_SPAM_ADDR version=2.55 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear sir, I am now using Autodock3.0. When I test the examples in autodock web file,(3PTB: Benzamidine docking to beta-Trypsin), I succeed in using autogrid, autotors and autodock command. I finally got the pdb file contains the docked conformations of the ligand. I want to add the macromolecule and the docked conformations together into one PDB file that contains everything. I find the answer in the FAQ (Frequently Asked Questions) page as following: % get-dockings mydocking.dlg % pdbqtopdb mymacromolecule.pdbqs >> mydocking.dlg.pdb However, when I run pdbqtopdb command, the error information is displayed: ---------------------------------------------------------- % pdbqtopdb 3ptb.pdbqs >> benA.3ptb.dlg.pdb awk: /home/xiong/autodock/dist305/share/pdbtopdb2.awk:49: fatal: Invalid range end: /[0-9][+- ]/ /home/xiong/autodock/dist305/share/fixatomnames: line 8: 4340 M I c { _ sed -f $AUTODOC K_UTI/fixatomnames.sed $* /home/xiong/autodock/dist305/share/getpdbrecords: line 2: 4338 M I c { _ egrep "^ATOM|^ HETATM|^REMARK|^USER|^END |^TER|^MODEL |^ENDMDL" $* ---------------------------------------------------------------- Could you please tell me why I can't get the pdb file contain the macromolecule and the docked ligand conformations? Thanks a lot ! Yours Sincerely Ying Xiong (my email address: xiongying99/at/fescomail.net) ---------------------------------------------------------------- FESCOmail.net From chemistry-request@ccl.net Mon Sep 15 03:00:42 2003 Received: from smtp.dmbr.UGent.be (dmbr242.fvms.ugent.be [157.193.189.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8F70ABS010481 for ; Mon, 15 Sep 2003 03:00:11 -0400 Received: from dmbr032.fvms.ugent.be (dmbr032.fvms.ugent.be [157.193.200.89]) by smtp.dmbr.UGent.be (Postfix) with ESMTP id 7646E68004; Mon, 15 Sep 2003 09:00:08 +0200 (CEST) Subject: Re: CCL:Autodock and Rigid Body Docking From: Dominique Vlieghe To: Chris Arthur Cc: CHEMISTRY In-Reply-To: <006d01c37a12$04f486c0$3b2ade89/at/chm.bris.ac.uk> References: <006d01c37a12$04f486c0$3b2ade89/at/chm.bris.ac.uk> Content-Type: text/plain; charset=UTF-8 Organization: Message-Id: <1063609110.8866.17.camel/at/dmbr032.fvms.ugent.be> Mime-Version: 1.0 X-Mailer: Ximian Evolution 1.2.4 Date: 15 Sep 2003 08:58:30 +0200 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=-4.9 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_XIMIAN version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi Chris, In AutoDock, the ligand is made flexible by defining the torsion angles that should vary. If you chose 0 torsion angles, your ligand would be regarded as being rigid. Furthermore, you can chose whichever torsion angle you desire to be kept flexible, as long as you do not have more than 32. This means about 8-16 side chains, depending on their size. Of course, the target will always be rigid... Someone else replied to you that ZDock is a good tool to do protein-protein docking. I agree with him when the two proteins have conformation very similar to the bound conformations. The perfomance however drops considerably when you work with homology models. I must say that I did not test RDock yet. Anyhow, I asked the more-or-less same question some time ago, and I got some rather nice responses. I have included the one I got from Garrett Morris: > > * A general question: > > I was wondering whether AutoDock is suitable for studying > > protein-protein interactions. In principle it is, but speed is the > > practical limitation I presume. Does anyone have experience with this? > > AutoDock was designed to dock flexible small molecules to > macromolecules, but I must admit to being pleasantly surprised to > discover that we have been able to use AutoDock successfully to perform > protein-protein docking. See, for example: > > Legge, G. B., G. M. Morris, et al. (2002). "Model of the alphaLbeta2 > integrin I-domain/ICAM-1 DI interface suggests that subtle changes in > loop orientation determine ligand specificity." Proteins 48(2): 151-60. > > Ollmann-Saphire, E., P. W. H. I. Parren, et al. (2001). "Crystal > Structure of a Neutralizing Human IgG Against HIV-1: a Template for > Vaccine Design." Science 293(5532): 1155-9. > > In these kinds of dockings, we compute grid maps with a spacing of 1C > and dimensions of 126C * 126C * 126C around the entire protein we are > docking to. The intention is to let the moving protein see the entire > surface of the fixed protein, and to allow enough room around the fixed > protein for the moving protein to fit within the grid. > > It is possible to allow selected sidechains in the moving protein to > change conformation during the docking, but these must be chosen within > the limit of the number torsions (32 by default). Which ones you choose > is an interesting question. > > There is a limit on the number of atoms in the moving molecule (2048, a > relic of the AutoDock source code's Fortran roots). This means if your > protein is very large (like the entire b12 antibody) you must truncate > the moving molecule to the domain(s) of interest. Alternatively, if you > have enough RAM on your machine, you can re-compile AutoDock with a > larger number of atoms ("MAX_ATOMS" in the "constants.h" file). Note > also that the more atoms there are to move during a docking, the longer > it will take to finish. > > One other thing to remember: for small molecule docking in AutoDock 3, > we use a small positive constant energy term in the hydrogen-bonding > (polar H and O) maps, that is designed to act as a penalty for any > hydrogen bonds not formed upon binding: a potential hydrogen bonding > atom that is in a hydrophobic, non-polar pocket is assumed to have lost > a hydrogen bond that it had before binding. This works well for small > molecules, but for proteins, which have hydrogen bonds _within_ their > structures both before and after binding, this one-size-fits-all > approach over-penalizes the polar H and O within the structures already > involved in hydrogen bonding. Thus, for proteins, mini-proteins and > other large macromolecules, we set these constants to zero. This is > done using the "constant" keyword in the GPF (grid parameter file). We > are addressing this simplification in future versions of AutoDock. > > I should make clear, it is not feasible to use AutoDock to dock a > protein-sized molecule with all possible torsions treated as rotatable: > aside from being computationally prohibitive with today's hardware, the > search space is vast, and not even Lamarckian Genetic Algorithms can > help. A reduced atom approach, on-lattice approximations and other > tricks are needed, and you start to enter protein folding territory. > > Our graphical user interface to AutoDock, ADT (AutoDockTools), also has > a way to set up a protein using the "Ligand" menu (it involves > selecting the residues you'd like to be flexible before choosing the > rotatable bonds). > > > > > * a more specific question: > > A way of circumventing a huge grid would be to use a smaller grid > > (assuming that the interacting residues must be 'close' to the > > receptor) > > and setting the extnrg parameters to 0.0 kcal mol-1 (meaning that atoms > > outside the grid would feel no field). Is this a correct assumption? > > Would this speed up the calculations? > > It could speed up the calculations (the energy calculation is O(N) > where N is the number of atoms in the moving molecule). There is also a > distance-dependent energy penalty for any atoms outside the grid box, > that is proportional to the sum of all the squares of the distances of > the atoms outside the grid to the centre of the grid. This is necessary > to drive 'escaping' molecules back towards the fixed molecule. I > haven't tried what you suggested, suspecting that the dockings will > give very high, positive energies, but I would encourage you to try and > see what happens. > > > > > Furthermore, are there other ways of avoiding the calculation of > > interactions involving ligand atoms that are too far away from the > > receptor? This would make sense, because in P-P interaction only a > > 'small' number of residues normally contribute to the interaction. Are > > they any ways of doing this in AutoDock? > > > > There is a non-bonded list in the AutoGrid calculation, but not in > AutoDock for the moving molecule: updating this during the docking > would slow down the calculation dramatically, and for small molecules, > the benefit did not out weight the cost. For proteins, there are tricks > you can play, and we are investigating them for future versions of > AutoDock. The simplest idea is to truncate the moving protein structure > manually before docking, but this introduces both 'prior knowledge' and > an artificial interface. It might be possible to 'hollow out' the > moving protein, but I fear this could deleteriously affect the > character of its electrostatic potential. On Sat, 2003-09-13 at 18:13, Chris Arthur wrote: > Hi > > I would like to try to dock a small protein (88aa) to a larger one (300ish > aa) - now I know autodock is really designed for small molecules but i was > wondering if there was any way to get it to essentially run a rigid body > dock of these two together? and if so, how i would go about it? or if thats > not possible to limit the flexibility of the small protein so that only > considers side chain rotation/flexibility and not the whole protein > > Thanks in advance > > Chris > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY/at/ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST/at/ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl/at/ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > Regards, Dominique -- ------------------------------ Dominique Vlieghe, Ph.D., Bioinformatics Core, Department for Molecular Biomedical Research (DMBR) VIB - Ghent University (new) 'Fiers-Schell-Van Montagu' building (new) Technologiepark 927 (new) B-9052 Ghent (Zwijnaarde), Belgium (new) Tel : +32-(0)9-33-13.693 (new) Fax : +32-(0)9-33-13.609 (new) email:dominique.vlieghe/at/dmbr.ugent.be (new) www:http://www.dmbr.ugent.be/ ------------------------------ From chemistry-request@ccl.net Mon Sep 15 05:24:29 2003 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8F9NuBS016548 for ; Mon, 15 Sep 2003 05:23:57 -0400 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailserver.unimi.it (iPlanet Messaging Server 5.2 Patch 1 (built Aug 19 2002)) with ESMTP id <0HL900CNJ0RXLW/at/mailserver.unimi.it> for chemistry/at/ccl.net; Mon, 15 Sep 2003 11:23:57 +0200 (MEST) Received: from heisenberg.chimica.unimi.it (heisenberg.chimica.unimi.it [159.149.240.30]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0HL900FLT0RVHV/at/smtp.unimi.it> for chemistry/at/ccl.net; Mon, 15 Sep 2003 11:23:56 +0200 (MEST) Date: Mon, 15 Sep 2003 11:33:32 +0200 From: Alessandro Contini Subject: G03 compilation under HP-UX To: CCL Message-id: <200309151133.32359.alessandro.contini/at/unimi.it> Organization: Istituto di Chimica Organica "Alessandro Marchesini" MIME-version: 1.0 Content-type: text/plain; charset=iso-8859-15 Content-disposition: inline User-Agent: KMail/1.5.3 X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_KMAIL version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h8F9OTBS016592 Hi, does anybody has a Makefile for compiling g03 under HP-UX? Any help will be grately appreciated. Greetings Alessandro Contini -- Alessandro Contini, Ph.D. Istituto di Chimica Organica "Alessandro Marchesini" Facolt` di Farmacia Universit` degli Studi di Milano Via Venezian, 21 20133 Milano Tel. +390250314480 Fax +390250314476 http://users.unimi.it/istchimorg/pagconthtm.htm ------------------------------------------------------------------- ------------------------------------------------------------------- This e-mail and any attachments is confidential and may contain attorney privileged information intended for the addressee(s) only. Reading, copying, disclosure or use by anybody else is unauthorised. If you are not the intended recipient, please delete this message and any attachments and advise the sender by return e-mail. ------------------------------------------------------------------- Il contenuto di questo messaggio elettronico e' riservato e tutelato dal segreto professionale ed e' rivolto eslusivamente al/ai destinatario/i identificato/i. Pertanto e' proibito leggerlo, copiarlo, divulgarlo o utilizzarlo da parte di chiunque salvo il/i destinatario/i. Se non siete il destinatario, vi invitiamo a cancellare il messaggio ed eventuali allegati dandocene immediatamente comunicazione scritta a mezzo posta elettronica. From chemistry-request@ccl.net Mon Sep 15 11:34:52 2003 Received: from cermm.concordia.ca (cermm.Concordia.CA [132.205.24.173]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8FFYKBS005724 for ; Mon, 15 Sep 2003 11:34:21 -0400 Received: from tau (tau.Concordia.CA [132.205.24.148]) by cermm.concordia.ca (8.11.6/8.11.6) with SMTP id h8FFYkd16941 for ; Mon, 15 Sep 2003 11:34:46 -0400 Message-ID: <000801c37bb8$7b97a300$9418cd84@tau> From: "wei yin" To: Subject: d-type functions for basis set 6-31G* in g98 Date: Mon, 15 Sep 2003 11:37:56 -0700 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0005_01C37B7D.CEF0EC90" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4927.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4927.1200 X-Spam-Status: No, hits=1.5 required=7.0 tests=DATE_IN_FUTURE_03_06,HTML_50_60,HTML_MESSAGE 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_0005_01C37B7D.CEF0EC90 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Is there anybody know if there is a differece of d-type functions for = basis set 6-31G* between gaussian98 and gaussian94? yin/at/cermm.concordia.ca ------=_NextPart_000_0005_01C37B7D.CEF0EC90 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Is there anybody know if there is a = differece of=20 d-type functions for basis set 6-31G* between gaussian98 and=20 gaussian94?
 
yin/at/cermm.concordia.ca<= /DIV>
 
------=_NextPart_000_0005_01C37B7D.CEF0EC90-- From chemistry-request@ccl.net Mon Sep 15 16:29:39 2003 Received: from webmail.mta.ca (postal.mta.ca [138.73.1.51]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h8FKT8BS020869 for ; Mon, 15 Sep 2003 16:29:08 -0400 Received: from nobody by webmail.mta.ca with local (Exim 4.20) id 19yzxa-0002u5-6p for chemistry)at(ccl.net; Mon, 15 Sep 2003 17:28:34 -0300 Received: from 138.73.24.166 ( [138.73.24.166]) as user kgdct)at(mailserv.mta.ca by webmail.mta.ca with HTTP; Mon, 15 Sep 2003 17:28:34 -0300 Message-ID: <1063657714.3f6620f22d7ed)at(webmail.mta.ca> Date: Mon, 15 Sep 2003 17:28:34 -0300 From: Katie Doucet To: chemistry)at(ccl.net Subject: free docking program MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Originating-IP: 138.73.24.166 X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) To whom it may concern; I was wondering if there was any freeware or at least free to academic institutions with the capability of DOCKING a substrate molecule inside an enzyme active site. If you know of any such a program could you please let me know. Thanks -k.Doucet Mount Allison University