From chemistry-request@ccl.net Mon Feb 21 09:36:39 2005 Return-Path: Received: from leitl.org (leitl.org [217.172.178.65]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1LEabut024218 for ; Mon, 21 Feb 2005 09:36:37 -0500 Received: by leitl.org (Postfix, from userid 500) id 1B7493A85E3; Mon, 21 Feb 2005 15:36:31 +0100 (CET) Date: Mon, 21 Feb 2005 15:36:30 +0100 From: Eugen Leitl To: chemistry * ccl.net Subject: [MMTK] MMTK 2.5.5 (fwd from khinsen * cea.fr) Message-ID: <20050221143630.GQ1404 * leitl.org> ----- Forwarded message from khinsen * cea.fr ----- From: khinsen * cea.fr Date: Mon, 21 Feb 2005 15:21:57 +0100 To: "mmtk * python.net list" Subject: [MMTK] MMTK 2.5.5 X-Mailer: Apple Mail (2.619.2) A new development release of MMTK, 2.5.5, is available now at the=20 standard locations. There are two new features that qualify as=20 experimental: the definition of molecules from within a Python script,=20 and the storage of molecular systems in XML files. The new module MMTK.MoleculeFactory permits the definition of groups=20 and molecules in terms of atoms, groups, and bonds. Coordinates and=20 attributes can be defined as well. See the example=20 Miscellaneous/molecule_factory.py for an illustration of its use. This=20 approach to molecule construction is complementary to the usual one of=20 writing database definition files. Depending on the application, one or=20 the other may be more practical. The XML file storage is a result of a discussion on an FSAtom mailing=20 list a while ago. The goal was the development of an XML interchange=20 format to be used by many molecular simulation packages. There was a=20 lively discussion about the format itself, but when the question turned=20 to actually implementing one in various programs, the list went silent. The format now implemented in MMTK is the last proposal I made on that=20 list. It uses CML tags as much as possible, though I won't claim that=20 it actually is CML, as CML is so huge that I never looked at all the=20 details of the definition. At the moment there is no other program that=20 uses the same format so its use for exchanging data is more than=20 limited. However, it can already be used to apply XML tools to=20 molecular systems definitions. If a concensus about an XML exchange=20 format ever evolves and gets implemented, I will probably modify MMTK's=20 XML code to use that format as well. To write any object (molecule, universe, ...) to an XML file, use the=20 method writeXML(). To read an XML file, use the module MMTK.XML and see=20 the example Miscellaneous/read_xml.py. Note that for reading XML files you must have the cElementTree module=20 installed. You can obtain it from =20 http://effbot.org/zone/celementtree.htm Konrad. -- --------------------------------------------------------------------- Konrad Hinsen Laboratoire L=E9on Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: khinsen * cea.fr --------------------------------------------------------------------- _______________________________________________ mmtk maillist - mmtk * starship.python.net http://starship.python.net/mailman/listinfo/mmtk From chemistry-request@ccl.net Mon Feb 21 18:02:46 2005 Received: from rassilon.bchs.uh.edu (Rassilon.BCHS.UH.EDU [129.7.238.206]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1LN2jut008332 for ; Mon, 21 Feb 2005 18:02:45 -0500 Received: by rassilon.bchs.uh.edu (Postfix, from userid 183) id C1EB95F81F0; Mon, 21 Feb 2005 16:07:26 -0600 (CST) From: tmahfouz ^^^ yahoo.com Reply-To: tmahfouz ^^^ yahoo.com To: chemistry ^^^ ccl.net Subject: Autodock tool does not add hydrogens properly. Date: Mon, 21 Feb 2005 16:07:26 -0600 User-Agent: KMail/1.7.2 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Content-Disposition: inline Message-Id: <200502211607.26493.tmahfouz ^^^ yahoo.com> X-Spam-Status: No, hits=5.5 required=7.5 tests=BAD_YAHOOMSGID, FORGED_YAHOO_RCVD,NO_REAL_NAME,VERYBAD_YAHOOMSGID autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello all, I'm trying to dock a small molecule to a protein. To add hydrogens to the protein I use adt and it works well except only one lysine residue it does not add the third hydrogen to it, all othe lysines have three hydrogens. Also, how to modify the protonation state of histidine residues to make some HD1 and some positively charged. Thanks, Tarek tmahfouz ^^^ yahoo.com From chemistry-request@ccl.net Tue Feb 22 06:08:12 2005 Received: from server.ccl.net (t157 [127.0.0.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1MB8BhU007714 for ; Tue, 22 Feb 2005 06:08:11 -0500 Received: (from apache@localhost) by server.ccl.net (8.12.8/8.12.8/Submit) id j1MB8B77007712 for chemistry :: ccl.net; Tue, 22 Feb 2005 06:08:11 -0500 Date: Tue, 22 Feb 2005 06:08:11 -0500 Message-Id: <200502221108.j1MB8B77007712 :: server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request :: ccl.net using -f From: "luciano, , marchi" To: chemistry :: ccl.net X-Web-Message-Number: 050222060527-7596 Subject: W:MOs display X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net hello, I am trying to visualize molecular orbitals (MOs) with Molden4.1 using the output from gaussian01. Is there any problem if I use the "gen" keyword and I specify my own basis set (lanl2dz for heavy atoms and 6-31+G for other atoms)? In fact I can actually display MOs but I am not sure if they are correct! the input is as follows: p b3lyp/gen density=current pop=(full, nboread) pseudo=read gfprint gfinput test scf=(MaxCycle=300) Symm(Int,Grad) Thank you, Luciano Marchio Department of Chemistry Universit di Parma, Parma Italy From chemistry-request@ccl.net Tue Feb 22 06:28:45 2005 Received: from relay.urv.es (relay.urv.es [193.144.16.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1MBShhU008750 for ; Tue, 22 Feb 2005 06:28:44 -0500 Received: from localhost (localhost [127.0.0.1]) by localhost.urv.es (Postfix) with SMTP id CB4D9A3A6 for ; Tue, 22 Feb 2005 12:28:42 +0100 (MET) Received: from [10.30.201.134] (dhcp30-51590.recerca.intranet.urv.es [10.30.201.134]) by relay.urv.es (Postfix) with ESMTP id 9B67AA3A6; Tue, 22 Feb 2005 12:28:37 +0100 (MET) Mime-Version: 1.0 Message-Id: Date: Tue, 22 Feb 2005 12:28:19 +0100 To: CHEMISTRY (a) ccl.net From: "D.BIO- Gerard Pujadas" Subject: CCL:Using AutoDock with more than the default number of points for dimension? Cc: gerard.pujadas (a) urv.net Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j1MBSkhU008759 Dear Autodock users, Is anybody running AutoDock with grids that have more than 128 points in, at least, one dimension? I found in this list that if I want to use AutoDock with grids that have more than the default number of points in at least one dimension, I need to edit the dist305/src/autodock/autocomm.h file and change "128" in "#define MAX_GRID_PTS 128" by the value that I want. I have done this, and I have recompilated AutoDock with 256 grid points (i.e. "#define MAX_GRID_PTS 256" in the dist305/src/autodock/autocomm.h file). Apparently, it runs without problems at first, but after some runs, a "Segmentation fault" mistake appears. This segmentation fault repeats even if I run AutoDock with little grid maps (i.e. 40 grid points in each dimension). The "Segmentation fault" problem only dissapears when I return the mentioned autocomm.h file to the original settings. Therefore, I wonder if one of you has succed to do that. May you be so kind to help me? With many thanks in advances Gerard -- ======================== NOTE: NEW ADDRESS AND E-MAIL ======================== Dr. Gerard Pujadas Grup de recerca en "Vi i Salut" Dept. Bioqummica i Biotecnologia room 106 Campus de Sant Pere Sescelades e-mail: gerard.pujadas (a) urv.net Univ. Rovira i Virgili phone: 34-977 559565 C/ Marcel7lm Domingo fax: 34-977 559597 43007 Tarragona (CATALONIA) State: Spain (European Union) =========================================================================== From chemistry-request@ccl.net Tue Feb 22 09:13:32 2005 Received: from web50410.mail.yahoo.com (web50410.mail.yahoo.com [206.190.38.245]) by server.ccl.net (8.12.8/8.12.8) with SMTP id j1MEDQhU016516 for ; Tue, 22 Feb 2005 09:13:26 -0500 Received: (qmail 93015 invoked by uid 60001); 22 Feb 2005 14:13:26 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=b+6yD7B8eLxUtPve2JSUBDVPzaW8mGMWVcDjsuGoK8o4pkwPsSCC5uTC6f1wK+4b6/rvNuY5N0KPgqWFhjOX19+q759g8RBH0f09dW0yACmyvAwaeeYJ6VmoSHMGI3okcbwc7m3oDGHG4OMHcwYkjy+Krj2VZWOXvat1uquX+g4= ; Message-ID: <20050222141326.93013.qmail _(a)_ web50410.mail.yahoo.com> Received: from [193.179.225.19] by web50410.mail.yahoo.com via HTTP; Tue, 22 Feb 2005 06:13:25 PST Date: Tue, 22 Feb 2005 06:13:25 -0800 (PST) From: Bruno Sopko Subject: Re: CCL:autodock3 on Linux To: Vemparala Satyavani , "D.BIO- Gerard Pujadas" Cc: CHEMISTRY _(a)_ ccl.net In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-1495709032-1109081605=:90911" X-Spam-Status: No, hits=1.2 required=7.5 tests=HTML_MESSAGE,MK_BAD_HTML_04, MY_MANY_BR autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --0-1495709032-1109081605=:90911 Content-Type: text/plain; charset=us-ascii Try to set stacksize to unlimited: in bash : ulimit -s ulimited set stacksize "ulimited" (hopefully) Bruno Sopko Vemparala Satyavani wrote: Gerard: Thanks for the Makefile.. I could compile it.. but sadly when i try to execute it, it fails giving a segmentation fault.. Vani On Mon, 21 Feb 2005, D.BIO- Gerard Pujadas wrote: > > Dear Vani, > > > > >I have been having problems trying to compile autodock on Linux > >machine..are there any suggestions? > >any particular flags i need to have/omit > > > > probably the problem is that you need a Makefile > adapted for a compilation in a Linux machine. I > am running AutoDock in a PC with Mandrake and I > did the following: > > 1) make clean > 2) make > > and that's all > > Please, use the Makefile I attached here and > replace with it the existing Makefile in > src/autodock folder. > > Hope this helps > > Gerard > -- > ======================== NOTE: NEW ADDRESS AND E-MAIL ======================== > Dr. Gerard Pujadas > Grup de recerca en "Vi i Salut" > Dept. Bioqummica i Biotecnologia room 106 > Campus de Sant Pere Sescelades e-mail: gerard.pujadas _(a)_ urv.net > Univ. Rovira i Virgili phone: 34-977 559565 > C/ Marcel7lm Domingo fax: 34-977 559597 > 43007 Tarragona (CATALONIA) > State: Spain (European Union) > =========================================================================== > -= 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 _(a)_ ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST _(a)_ 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, jlabanow _(a)_ nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com --0-1495709032-1109081605=:90911 Content-Type: text/html; charset=us-ascii
Try to set stacksize to unlimited:
in bash : ulimit -s ulimited
set stacksize "ulimited" (hopefully)
 
Bruno Sopko

Vemparala Satyavani <vani _(a)_ reef.phys.lsu.edu> wrote:

Gerard:

Thanks for the Makefile.. I could compile it.. but sadly when i try to
execute it, it fails giving a segmentation fault..

Vani
On Mon, 21 Feb 2005, D.BIO- Gerard Pujadas wrote:

>
> Dear Vani,
>
> >
> >I have been having problems trying to compile autodock on Linux
> >machine..are there any suggestions?
> >any particular flags i need to have/omit
> >
>
> probably the problem is that you need a Makefile
> adapted for a compilation in a Linux machine. I
> am running AutoDock in a PC with Mandrake and I
> did the following:
>
> 1) make clean
> 2) make
>
> and that's all
>
> Please, use the Makefile I attached here and
> replace with it the existing Makefile in
> src/autodock folder.
>
> Hope this helps
>
> Gerard
> --
> ======================== NOTE: NEW ADDRESS AND E-MAIL ========================
> Dr. Gerard Pujadas
> Grup de recerca en "Vi i Salut"
> Dept. Bioqummica i Biotecnologia room 106
> Campus de Sant Pere Sescelades e-mail: gerard.pujadas _(a)_ urv.net
> Univ. Rovira i Virgili phone: 34-977 559565
> C/ Marcel7lm Domingo fax: 34-977 559597
> 43007 Tarragona (CATALONIA)
> State: Spain (European Union)
> ===========================================================================
>




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http://mail.yahoo.com --0-1495709032-1109081605=:90911-- From chemistry-request@ccl.net Tue Feb 22 01:41:58 2005 Received: from web51310.mail.yahoo.com (web51310.mail.yahoo.com [206.190.38.176]) by server.ccl.net (8.12.8/8.12.8) with SMTP id j1M6fuut026978 for ; Tue, 22 Feb 2005 01:41:56 -0500 Received: (qmail 99651 invoked by uid 60001); 22 Feb 2005 06:41:56 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=zAd33atFiyS3cmU03aRRY2CV5WrhsSat4HbctGta/CqxTO6D9AhWdxK1ef7y8kQ+proMsHsEdAY0SrLvE94DE5OYwvcW9CLKJmqcenG1ZMGYPYcIt2vsG1qYK5yms2wt8OJFjarPUmGuWRDaS3Powgn97aWqwgl0mLhaknnOgZ4= ; Message-ID: <20050222064156.99649.qmail = web51310.mail.yahoo.com> Received: from [24.152.170.75] by web51310.mail.yahoo.com via HTTP; Mon, 21 Feb 2005 22:41:55 PST Date: Mon, 21 Feb 2005 22:41:55 -0800 (PST) From: Sengen Sun Subject: CCL: my final posting on orbitals and reality? To: chemistry = ccl.net In-Reply-To: <006101c5180c$cea1edc0$043010ac@suntur> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=1.1 required=7.5 tests=RCVD_IN_DSBL autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --- Jorge Seminario wrote: > Dear Prof. Sengen Sun, > Yes, orbitals are humanly defined as any other > definition. > Certainly, some of the definitions of MOs are better > than > others for expressing or representing observations > of reality > (experiments). So as long as you accept that MOs > are just > definitions (explicitly or implicitly) and that > humans have > the freedom to define them in different ways, and > not just > constrained to one book, school, or interpretation, > some > of these MO definitions might reflect acceptable, > not necessarily > precise, observed features. Thus you can associate > some of the > MO definitions to an observed feature (reality). > Cordially > Jorge > It would be more accurate to say that any physical properties are directly associated with electron density and electrons' kinetic motion other than single orbitals. Especially in multielectron systems, it is impossible to me that any observable properties can be CONCEPTUALLY assinged to specific orbitals, although orbitals are very valuable in mathematical treatments. I just realize that it is hard to argue whether you can associate some of the MO to an observed feature. This question is dualistic depending how you think. If you answer yes to this question, what you really mean is to conduct mathematical correlations between physical properties and orbitals. This is perfectly fine to me. This does not make orbitals a physical observable! At the most, what you can safely say is to build an artificial image of orbitals. What is the point to argue about this? Dr. Scerri started this 5 years ago, while I had had a long standing problem to understand the mechanism of concerted cycloadditions. After I studied Dr. Scerri's philosphy for a couple of years, I started to realize that I must support his philosophical arguments. As indicated in a quote given in Dr. Spanget-Larsen's posting on Jan. 20, "it is very dangerous to assume that such a limited theory can then be used in a wider sense. We must be very careful to ask proper questions of our theories or we face the danger of being greatly misled." Given such a situation of divided opinions in the scientific community, it is meaningful to make some effort and to seek some common ground or to form some possible conventions about how to express our theories and experiments. This could help our students understand, and scientists understand each other. Towards such a goal, I have made my own small effort. Forgive me for my bad emotion and harsh languages I used from time to time. I don't mind anything else as soon as we have something to discuss about science. Every one's opinions deserve being respected. I hope every one will continue to pursue what he or she believes to be correct. What I am really proud of is that all the ordinary scientists have the opportunities to express themselves in the stage of a scientific party on Internet. This is the further civilization of our human beings. I hope this is my final posting to this thread although I may continue to have fun by working on some mechanisms of organic chemical reactions. Thanks every one. Sengen __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com