From chemistry-request@server.ccl.net Tue Oct 22 05:46:27 2002 Received: from mta1.sucs.soton.ac.uk ([152.78.128.140]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9M9kRN09007 for ; Tue, 22 Oct 2002 05:46:27 -0400 Received: from soton.ac.uk (scarlet.chem.soton.ac.uk [152.78.196.193]) (authenticated bits=0) by mta1.sucs.soton.ac.uk (8.12.3/8.12.3) with ESMTP id g9M9kDPA016855 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NO); Tue, 22 Oct 2002 10:46:16 +0100 Sender: L.BENASSI@soton.ac.uk Message-ID: <3DB51E60.E383DABB@soton.ac.uk> Date: Tue, 22 Oct 2002 10:46:08 +0100 From: Luca Fenu Organization: university of southampton X-Mailer: Mozilla 4.79 [en] (X11; U; Linux 2.4.20-pre9 i686) X-Accept-Language: en MIME-Version: 1.0 CC: chemistry@ccl.net Subject: Hydrogen Bond models References: <000f01c27900$8cbd43d0$630dfa8d@mc> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-MailScanner: Believed to be clean X-MailScanner-Spam: not spam (whitelisted), SpamAssassin (score=0.4, required 5, DEAR_SOMEBODY, MISSING_HEADERS) Dear All, I'm going to code the interaction between a ligand and a protein, including H-Bonding. Could someone suggest me to a good paper/review about Hydrogen bond models between biological macromolecules? many thanks luca From chemistry-request@server.ccl.net Tue Oct 22 10:15:07 2002 Received: from leviathan.ele.uri.edu ([131.128.51.64]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9MEF7N16376 for ; Tue, 22 Oct 2002 10:15:07 -0400 Received: from ele.uri.edu (ip68-9-19-36.ri.ri.cox.net [68.9.19.36]) by leviathan.ele.uri.edu (8.12.2/8.12.2) with ESMTP id g9MEF598023806; Tue, 22 Oct 2002 10:15:05 -0400 (EDT) Message-ID: <3DB55D02.3030805@ele.uri.edu> Date: Tue, 22 Oct 2002 10:13:22 -0400 From: Su Wu User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; rv:0.9.4.1) Gecko/20020314 Netscape6/6.2.2 X-Accept-Language: en-us MIME-Version: 1.0 To: Luca Fenu CC: chemistry@ccl.net Subject: Re: CCL:Hydrogen Bond models References: <000f01c27900$8cbd43d0$630dfa8d@mc> <3DB51E60.E383DABB@soton.ac.uk> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hello, I happen to have the same question about H-Bonding. A good book about H-Bonding is by George Jeffrey, "An Introduction to Hydrogen-Bonding", Oxford, 1997, pp.303. He and Saenger, W. wrote another good one in 1991, Springer. But I don't have any good review paper. I would like to know if somebody knows. Thanks, Su Luca Fenu wrote: >Dear All, > >I'm going to code the interaction between a ligand and a protein, >including H-Bonding. Could someone suggest me to a good paper/review >about Hydrogen bond models between biological macromolecules? many >thanks > > luca > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Tue Oct 22 04:38:04 2002 Received: from hotmail.com ([64.4.37.107]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9M8c4N07671 for ; Tue, 22 Oct 2002 04:38:04 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Tue, 22 Oct 2002 01:38:04 -0700 Received: from 132.187.70.201 by pv2fd.pav2.hotmail.msn.com with HTTP; Tue, 22 Oct 2002 08:38:03 GMT X-Originating-IP: [132.187.70.201] From: "lala podibaer" To: chemistry@ccl.net Subject: rotate molecules along princliple moments of inertia Date: Tue, 22 Oct 2002 08:38:03 +0000 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1; format=flowed Message-ID: X-OriginalArrivalTime: 22 Oct 2002 08:38:04.0253 (UTC) FILETIME=[567F98D0:01C279A6] Hi all, I have a problem concerning the alignment of molecules along their principle moments of inertia. I read through several papers and use now a singular value decomposition for the alignment. At first glance everything seems to be ok with the rotated molecules, they are nicely aligned along the axes and insensitive to rotation. Unfotunately, at closer inspection of the aligned molecules it can be found that some of the molecules are rather mirrored than rotated along the principle axes. I think the problem lies within the sorting routine of the eigenvalues. Since the eigenvectors are not sorted according to the largest value in the xyz coordinates, multiplication of the original X matrix with the eigenvectors doesn't necessarily produce rotated but mirrored molecules. I am pretty certain that this problem has already been solved, but I was not able to find any documentation in terms of formulas which I could use for implementation. I would appreciate every reference or subroutine that might help me with this. Cheers Mike _________________________________________________________________ Messenger  -  Wer in Echtzeit kommunizieren will, lädt den MSN Messenger. Cool, kostenlos und mit 3D Emoticons: http://messenger.msn.de From chemistry-request@server.ccl.net Tue Oct 22 06:49:41 2002 Received: from resu1.ulb.ac.be ([164.15.59.200]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9MAnVN10404 for ; Tue, 22 Oct 2002 06:49:36 -0400 Received: from mach.vub.ac.be (mach.ulb.ac.be [164.15.128.3]) by resu1.ulb.ac.be (8.8.8/3.17.1.ap (resu)) id MAA13328; Tue, 22 Oct 2002 12:47:16 +0200 (MEST) for From: cbiot@ulb.ac.be Received: from ulb.ac.be (chimorg-pc5.ulb.ac.be [164.15.61.104]) by mach.vub.ac.be (8.9.3/3.13.3.ap (mach)) id MAA18178; Tue, 22 Oct 2002 12:49:21 +0200 (MET DST) for Message-ID: <3DB549CC.5000204@ulb.ac.be> Date: Tue, 22 Oct 2002 12:51:24 +0000 Organization: ULB User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4) Gecko/20011126 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: Luca Fenu CC: chemistry@ccl.net Subject: Re: CCL:Hydrogen Bond models References: <000f01c27900$8cbd43d0$630dfa8d@mc> <3DB51E60.E383DABB@soton.ac.uk> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi, just have a look at this book: Hydrogen Bonding in Biological Structures by GA Jeffrey and W Saenger Springer Verlag 1994 have a nice day.... Luca Fenu wrote: > Dear All, > > I'm going to code the interaction between a ligand and a protein, > including H-Bonding. Could someone suggest me to a good paper/review > about Hydrogen bond models between biological macromolecules? many > thanks > > luca > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > > -- ******************************************************* Dr. BIOT Christophe Ingenierie Biomoleculaire, CP 165/64 Universite Libre de Bruxelles 50, Av. F. Roosevelt B-1050 Bruxelles Belgique Phone: 32-2-650 3001 Fax: 32-2-650 3606 E-mail:cbiot@ulb.ac.be http://babylone.ulb.ac.be/~christophe/ http://www.ulb.ac.be/rech/inventaire/unites/ULB163.html ******************************************************* From chemistry-request@server.ccl.net Tue Oct 22 04:54:35 2002 Received: from mailbox.engr.sc.edu ([129.252.21.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9M8sYN07936 for ; Tue, 22 Oct 2002 04:54:34 -0400 Received: from Amaru (viru.ee.sc.edu [129.252.22.140]) by mailbox.engr.sc.edu with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2656.59) id T5HFQWGZ; Tue, 22 Oct 2002 04:54:34 -0400 Message-ID: <015801c279a8$a42f5ff0$8c16fc81@Amaru> Reply-To: "Roy Araujo" From: "Roy Araujo" To: Subject: Au parameters Date: Tue, 22 Oct 2002 04:54:29 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0155_01C27987.1A976330" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2720.3000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0155_01C27987.1A976330 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello: Does anyone know where could I get the AM1 and/or PM3 parameters for gold (Au). If any, I would like to implement them in MOPAC 2002. Roy Araujo USC Columbia, SC 29208 raraujo@engr.sc.edu ------=_NextPart_000_0155_01C27987.1A976330 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello:
Does=20 anyone know where could I get the AM1 and/or PM3 parameters for
gold = (Au). If=20 any, I would like to implement them in MOPAC 2002.
 
Roy Araujo
USC
Columbia, SC = 29208
raraujo@engr.sc.edu
------=_NextPart_000_0155_01C27987.1A976330-- From chemistry-request@server.ccl.net Tue Oct 22 12:36:59 2002 Received: from cornell.edu ([132.236.56.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9MGaxN21811 for ; Tue, 22 Oct 2002 12:36:59 -0400 Received: from cornell.edu (lock.lassp.cornell.edu [128.84.241.198]) by cornell.edu (8.9.3/8.9.3) with ESMTP id MAA22368 for ; Tue, 22 Oct 2002 12:36:58 -0400 (EDT) Sender: cc236@cornell.edu Message-ID: <3DB57EAA.9F9D5FAA@cornell.edu> Date: Tue, 22 Oct 2002 12:36:58 -0400 From: Connie Chang X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.2.19-6.2.16smp i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Gaussian98 What's the usefulness of Forces keyword? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all -- I'm trying to do a series of single point calculations with the aim of getting the forces for all the cartesian components of my atoms positions. My question is, what is the purpose of the Forces keyword? I thought that if you ask Gaussian to perform a single point calculation using a semi-empirical method, that this already gives you the gradients (and forces are just the negative of these). Am I missing something here? Thanks, Connie From chemistry-request@server.ccl.net Tue Oct 22 21:35:04 2002 Received: from cse.nd.edu ([129.74.25.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9N1Z4N10544 for ; Tue, 22 Oct 2002 21:35:04 -0400 Received: from dylan.cse.nd.edu (ako@dylan.cse.nd.edu [129.74.32.170]) by cse.nd.edu (8.11.2/8.11.2) with ESMTP id g9N1Z0w26026 for ; Tue, 22 Oct 2002 20:35:00 -0500 (EST) Received: from localhost (ako@localhost) by dylan.cse.nd.edu (8.11.2/8.10.1) with ESMTP id g9N1Yv315761 for ; Tue, 22 Oct 2002 20:34:57 -0500 (EST) Date: Tue, 22 Oct 2002 20:34:57 -0500 (EST) From: Alice NgarKit Ko To: chemistry@ccl.net Subject: PDB file editing Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I would like to know if there is an easy way to edit a PDB file. I loaded the structure into VMD for viewing. There are a lot of water molecules that have traveled far from where I wanted them. I hope I can use some program where I can just pick and delete the water molecules and then write out the remaining atoms to a new PDB file. If anyone knows how to do this, please let me know. Thank you very much Alice From chemistry-request@server.ccl.net Tue Oct 22 15:00:56 2002 Received: from rutchem.rutgers.edu ([128.6.1.216]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9MJ0uN26020 for ; Tue, 22 Oct 2002 15:00:56 -0400 Received: (from xiangjun@localhost) by rutchem.rutgers.edu (8.9.3/8.9.3) id PAA2986593; Tue, 22 Oct 2002 15:00:55 -0400 (EDT) Date: Tue, 22 Oct 2002 15:00:55 -0400 (EDT) Message-Id: <200210221900.PAA2986593@rutchem.rutgers.edu> From: Xiang Lu To: angelschnur@hotmail.com CC: chemistry@ccl.net Subject: Re: CCL:rotate molecules along princliple moments of inertia Reply-to: xiangjun@rutchem.rutgers.edu Dear Mike: I believe your problem arises because of the ambiguity in selecting the "direction" of the eigenvectors. Let the first and second eigenvectors be whatever you have, you need to make sure the third one is the cross product of the first two, thus ensuring a right-handed coordinate system. "rotate_mol", a utility in 3DNA (http://rutchem.rutgers.edu/~xiangjun/3DNA/), can do this and a bit more, and it is used to get the most extended views for every structure in the updated Nucleic Acid Database (NDB) (http://beta-ndb.rutgers.edu/). Hope this helps. Xiang-Jun -- Dr. Xiang-Jun Lu | Tel: (732) 445 4619 (O) Department of Chemistry | Rutgers University | Fax: (732) 445 5958 610 Taylor Road | Email: xiangjun@rutchem.rutgers.edu Piscataway, NJ 08854-8087 | URL: http://rutchem.rutgers.edu/~xiangjun/ >>>>> "lala" == lala podibaer writes: lala> Hi all, lala> I have a problem concerning the alignment of molecules along their principle lala> moments of inertia. I read through several papers and use now a singular lala> value decomposition for the alignment. At first glance everything seems to lala> be ok with the rotated molecules, they are nicely aligned along the axes and lala> insensitive to rotation. Unfotunately, at closer inspection of the aligned lala> molecules it can be found that some of the molecules are rather mirrored lala> than rotated along the principle axes. lala> I think the problem lies within the sorting routine of the eigenvalues. lala> Since the eigenvectors are not sorted according to the largest value in the lala> xyz coordinates, multiplication of the original X matrix with the lala> eigenvectors doesn't necessarily produce rotated but mirrored molecules. lala> I am pretty certain that this problem has already been solved, but I was not lala> able to find any documentation in terms of formulas which I could use for lala> implementation. lala> I would appreciate every reference or subroutine that might help me with lala> this. lala> Cheers lala> Mike