From chemistry-request@server.ccl.net Mon Dec 9 01:01:06 2002 Received: from gip2.u-picardie.fr ([193.49.184.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB9615i19930 for ; Mon, 9 Dec 2002 01:01:05 -0500 Received: by gip2.u-picardie.fr (Postfix, from userid 33) id B83B59211; Mon, 9 Dec 2002 07:00:52 +0100 (CET) To: chemistry@ccl.net Subject: Standard orientation in g98 Message-ID: <1039413652.3df43194ac12a@webmail.u-picardie.fr> Date: Mon, 09 Dec 2002 07:00:52 +0100 (CET) From: FyD MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.6 Dear All, In gaussian98: If I use the keyword CalcHFFC for an optimization, the Standard Deviation Cartesian coordinates for the optimized structure is NOT printed in the g98 ouput (the structure converges very quickly after step 1 of the optimization). On the contrary, it is always printed if I do not use CalcHFFC or if the optimization convergence takes several steps. Is there a command to force the "Standard Deviation Cartesian coordinates" for the optimized structure to be printed in the output ? Thanks, regards, Francois From chemistry-request@server.ccl.net Mon Dec 9 04:01:55 2002 Received: from smtp.relc.com ([194.183.162.130]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB991qi23255 for ; Mon, 9 Dec 2002 04:01:52 -0500 Received: from gw.imbg.org.ua (gw.imbg.org.ua [194.183.176.94]) by smtp.relc.com (8.12.6/8.12.6) with ESMTP id gB991ZJQ016888 for ; Mon, 9 Dec 2002 11:01:42 +0200 (EET) Received: from violet (violet.imbg.org.ua [10.0.5.80]) by gw.imbg.org.ua (8.12.6/8.11.6) with ESMTP id gB99HeXX050763 for ; Mon, 9 Dec 2002 11:17:40 +0200 (EET) (envelope-from dikov@imbg.org.ua) From: Dmitry Kovalsky Reply-To: dikov@imbg.org.ua Organization: IMBG To: CHEMISTRY@ccl.net Subject: Re: CCL:ion concentration in protein simulation Date: Mon, 9 Dec 2002 11:00:52 +0200 User-Agent: KMail/1.4.7 References: In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Content-Disposition: inline Message-Id: <200212091100.52254.dikov@imbg.org.ua> X-AVP-RU: Passed Dear Pete Gannett, I have enconterd the same problem and my results are not the same as experimental one. Did you try to use only counterions and to compare the MD results vs that with salt? How you prepared your system with salt? Thanks in advance Sincerely yours, Ph.D. Student Dmitry Kovalsky Institute of Molecular Biology & Genetics 150 Akad. Zabolotnogo Street, Kiev-143, 03143 UKRAINE E-mail: dikov@imbg.org.ua Fax: +380 (44) 266-0759 Tel.: +380 (44) 266-5589 From chemistry-request@server.ccl.net Mon Dec 9 12:24:52 2002 Received: from lauca.usach.cl ([158.170.64.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB9HOpi15121 for ; Mon, 9 Dec 2002 12:24:51 -0500 Received: from danilo ([158.170.51.186]) by lauca.usach.cl (8.11.6/8.11.6) with SMTP id gB9HIUH21884 for ; Mon, 9 Dec 2002 14:18:30 -0300 From: "Danilo Gonzalez" To: Subject: ATP-Mg2+ CHARMM Date: Mon, 9 Dec 2002 14:22:47 -0300 Message-ID: <001d01c29fa7$97c4b100$ba33aa9e@usach.cl> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Hi all, Somebody have some good tips for set the parameter of complex ATP-Mg2+ in charmm? Charmm27 have some parameters for ATP, but,.. how I can make the bond between Mg and the Oxygens of ATP and the waters coordinated?, Thanks a lot for any help. Best regards, Dr. Danilo Gonzalez University of Santiago of Chile Faculty of Chemistry and Biology Casilla 40, Correo 33, Santiago - Chile. From chemistry-request@server.ccl.net Mon Dec 9 20:38:13 2002 Received: from yakko.cimav.edu.mx ([148.223.46.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBA1cCi23903 for ; Mon, 9 Dec 2002 20:38:12 -0500 Received: from LAQUICOM02 (mild.cimav.edu.mx [148.223.46.1]) by yakko.cimav.edu.mx (8.11.6/8.11.2) with SMTP id gBA2S9R27349 for ; Mon, 9 Dec 2002 19:28:09 -0700 Message-ID: <010c01c29fe4$c16e8200$8400000a@LAQUICOM02> From: "Dr. Daniel Glossman-Mitnik" To: Subject: program for the calculation of ring centers Date: Mon, 9 Dec 2002 18:40:36 -0600 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0109_01C29FB2.76809AD0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 Disposition-Notification-To: "Dr. Daniel Glossman-Mitnik" X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0109_01C29FB2.76809AD0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear netters: Where can I find a program for the calculation of molecular ring centers in order to be used in the determination of aromaticity according to the NICS criteria ? Thanks in advance. Dr. Daniel Glossman-Mitnik *************************************************************************= *** Dr. Daniel Glossman-Mitnik Centro de Investigacion en Materiales Avanzados (CIMAV) LAQUICOM - Laboratorio de Quimica Computacional Miguel de Cervantes 120 - Complejo Industrial Chihuahua Chihuahua, Chih. 31109 - Mexico Phone: (52) 614 4391151 FAX: (52) 614 4391112 E-mail: daniel.glossman@cimav.edu.mx glossman@hotmail.com dglossman@yahoo.com *************************************************************************= *** ------=_NextPart_000_0109_01C29FB2.76809AD0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
 
Dear netters:
 
Where can I find a program for the = calculation of=20 molecular ring
centers in order to be used in the = determination of=20 aromaticity
according to the NICS criteria = ?
 
Thanks in advance.
 
          &nbs= p;            = ;            = =20 Dr. Daniel Glossman-Mitnik
 
 
****************************************************************= ************
Dr.=20 Daniel Glossman-Mitnik
Centro de Investigacion en Materiales = Avanzados=20 (CIMAV)
LAQUICOM - Laboratorio de Quimica Computacional
Miguel de=20 Cervantes 120 - Complejo Industrial Chihuahua
Chihuahua, Chih. 31109 = -=20 Mexico
Phone: (52) 614 4391151      FAX: = (52) 614=20 4391112
E-mail: daniel.glossman@cimav.edu.mx=
           = ;=20 glossman@hotmail.com
 &n= bsp;         =20 dglossman@yahoo.com
**********= ******************************************************************=
------=_NextPart_000_0109_01C29FB2.76809AD0-- From chemistry-request@server.ccl.net Mon Dec 9 04:14:50 2002 Received: from tigris.klte.hu ([193.6.138.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB99Eni24732 for ; Mon, 9 Dec 2002 04:14:49 -0500 Received: from cthulhu (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP; Mon, 9 Dec 2002 10:13:52 +0100 Message-ID: <001001c29f64$030a7c40$3b8506c1@cthulhu> From: "Tamas E. Gunda" To: , Subject: Re:CCL:pdb compatibility Date: Mon, 9 Dec 2002 10:19:01 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4920.2300 X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4920.2300 Hi, I think the problem with heavy atoms in PDB files may lay in the exact syntax and structure of PDB files. It it is not easy to describe here, as most mailing programs cut long lines, but I give a try. According to PDB file rules, atom names occupy columns 13-16. If it is an atom name, such as CA (C-alpha) in peptides, it must be in pos. 14-15. If it is a heavy atom, it is left aligned, i.e. it occupies pos. 13-14: "_ CA_ " for C alpha, "CA __ " for calcium (and other heavy atoms). There are several programs, which do not take into account this rule. To avoid this ambiguity in the new PDB version (>2) the elemental symbols should be at the end of lines, cols. 77-78, but again, some programs don't consider this. But one more problem: All coordinate lines should begin with the ATOM token, if the atom is included in an "official" residue (such as GLY, ALA etc). In these lines heavy atoms should occure In case of "unofficial" residues or elements the lines should begin with HETATM. Sometimes this also gets mixed, and then it is difficult for a program to find out that CD is a side chain carbon or cadmium. So if heavy atoms are misinterpreted, it is advisable to check them and correct manually, if necessary. I have a small graphical representation of the different PDB file structures, maybe it proves useful. See: http://www.klte.hu/~gundat/m2m/PDB_file_small.gif Tamas ----- Original Message ----- From: "Ioana Cozmuta" To: "John Bushnell" Cc: Sent: Saturday, December 07, 2002 03:30 Subject: CCL:pdb compatibility > Hi, > > THanks for your reply. I've already tried to use the protonate utility in > amber by removing the hydrogens from the structure and letting the program > add them back. The problem seems to be in the names of the heavy atoms, > they seem to be incompatible as well. > > Ioana > > > On Fri, 6 Dec 2002, John Bushnell wrote: > > > > > For converting pdb files for input to Amber, use the 'protonate' > > utility. It's under Miscellaneous in the Amber 7 manual. We > > recently found that using this very simple translator got rid > > of all sorts of problems reading Brookhaven pdb files. I hope > > it works for your InsightII files (which I have no experience > > with). > > > > HTH - John > > > > On Fri, 6 Dec 2002, Ioana Cozmuta wrote: > > > > > > > > Hi, > > > > > > And a second question for today. > > > I am generating a pdb file with InsightII (MSI software) and I am trying > > > to read it in amber (leap). However it seems that there is > > > quite a difference between the ways InsightII writes a pdb file and what > > > amber knows to read. I am not sure but the main difference seems to be > > > that InsightII is writing the pdb file using Brokhaven nomenclature while > > > amber needs the IUPAC names. > > > I am sure this is a frequent encountered problem and that there should be > > > simple ways around. I tried to use babel and WHAT IF to correct for the > > > differences but both failed. > > > I would appreciate your help. > > > > > > Thank you, > > > Ioana From chemistry-request@server.ccl.net Mon Dec 9 04:10:24 2002 Received: from mailstudenti.unimi.it ([159.149.10.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gB99ANi24610 for ; Mon, 9 Dec 2002 04:10:23 -0500 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailstudenti.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0H6U00DA7HH435@mailstudenti.unimi.it> for CHEMISTRY@ccl.net; Mon, 09 Dec 2002 10:10:17 +0100 (MET) Received: from Villa (villa.farma.unimi.it [159.149.79.66]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with SMTP id <0H6U00EHIHH5DY@smtp.unimi.it> for CHEMISTRY@ccl.net; Mon, 09 Dec 2002 10:10:17 +0100 (MET) Date: Mon, 09 Dec 2002 10:12:45 +0100 From: Giulio Vistoli Subject: Re: CCL:file formats/mol. medels; was:V3000 molfile format To: petitjean@itodys.jussieu.fr, CHEMISTRY@ccl.net Message-id: <000f01c29f63$23162df0$424f959f@Villa> Organization: =?iso-8859-1?Q?Universit=E0_di_Milano?= MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 X-Mailer: Microsoft Outlook Express 6.00.2800.1106 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT X-Priority: 3 X-MSMail-priority: Normal References: <02120613563688@itodys.jussieu.fr> We are tackling the problem of file formats for several years and our software VEGA (http://www.ddl.unimi.it) is now recognized as one of the most interesting product to handle and manage the molecular files. In this product we have implemented some features that could aid the use of file formats: - PDBFat format: this format was created in order to include extra information keeping the compatibility with the Brookhaven National Library specifications. For this reason, a sequence of REMARK records (one for each atom) was added at the beginning of file. The REMARK type is the user defined REMARK 77 (see PDB specifications) followed by the EXTRA keyword. In these extra lines you can add several information that will be read by specific programs, while the other softwares will skip these remark lines without any compatibility problems. - The Interchange File Format (IFF) is a binary file with an chunk structure (like IFF-ILBM, AIFF, etc). All chunks are optional (with the exception of the first) and the structure is totally expandable. With this powerful format you can store the maximum number of information and VEGA uses this format to save several ancillary information (like, atom color, atom selected, labels, measures, rototranslations, etc) that could not be saved with other formats. - ATDL language allows to define atom types. With ATDL you can describe any atom specification and you can add new force field templates so that VEGA can recognize them assigning the atom types and atomic charges. Using ATDL you can both convert file formats and change the force field assignment. Moreover we think that a software like VEGA, cannot be a black box, but it must be a totally expandable program so that everyone can add specific functions for particular purposes. For this reason we improve VEGA with two systems to develop new VEGA features: a plug-in architecture and a script language. On this ground the user can utilize the already existent VEGA functions as a pieces of code to build new features. Finally we are very interested to know the opinions and requirements of the people that must work with the plethora of formats that invaded the molecular modelling and we think that the definition of a standard format, usable for the standard applications, is a problem that we must try to resolve as soon as possible. Giulio Vistoli -------------- Giulio Vistoli Istituto di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano Italia Tel. +39-02-50317545 Fax +39-02-50317565 giulio.vistoli@unimi.it http://www.ddl.unimi.it From chemistry-request@server.ccl.net Mon Dec 9 22:28:42 2002 Received: from mtiwmhc11.worldnet.att.net ([204.127.131.115]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBA3Sfi25569; Mon, 9 Dec 2002 22:28:42 -0500 Received: from daveg.cachesoftware ([12.89.128.130]) by mtiwmhc11.worldnet.att.net (InterMail vM.5.01.05.12 201-253-122-126-112-20020820) with ESMTP id <20021210032833.ULBJ9286.mtiwmhc11.worldnet.att.net@daveg.cachesoftware>; Tue, 10 Dec 2002 03:28:33 +0000 Message-Id: <5.2.0.9.0.20021209185047.029ae6f0@mail.cachesoftware.com> X-Sender: X-Mailer: QUALCOMM Windows Eudora Version 5.2.0.9 Date: Mon, 09 Dec 2002 19:04:54 -0800 To: chemistry@ccl.net, chemistry-request@ccl.net From: David Gallagher Subject: CAChe TrainingCourse: February 3-6, 2003 Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_14679308==.ALT" --=====================_14679308==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed CAChe Training: February 3-6, 2003 The next CAChe Advance Training Course will be held at the CAChe Group offices in Portland, Oregon on February 3rd to 6th, 2003, just an hours drive from the Mount Hood ski resorts. Topics covered will include: reaction modelling and thermo-chemistry, Quantitative Structure-property Relationships (QSPR/QSAR), Conformation Searching, UV-visible spectra, prediction of physical, chemical and biological properties, protein and medicinal chemistry, and polymer properties. Over half the time is set aside for hands-on lab exercises. More information is available at www.CACheSoftware.com or from Kristin Briggs at 1 503 746 3602, . David Gallagher CAChe Group, Fujitsu --=====================_14679308==.ALT Content-Type: text/html; charset="us-ascii"         CAChe Training:   February 3-6, 2003

The next CAChe Advance Training Course will be held at the CAChe Group offices in Portland, Oregon on February 3rd to 6th, 2003, just an hours drive from the Mount Hood ski resorts.

Topics covered will include: reaction modelling and thermo-chemistry, Quantitative Structure-property Relationships (QSPR/QSAR), Conformation Searching, UV-visible spectra, prediction of physical, chemical and biological properties, protein and medicinal chemistry, and polymer properties. Over half the time is set aside for hands-on lab exercises.

More information is available at www.CACheSoftware.com or from Kristin Briggs at 1 503 746 3602, <kbriggs@CACheSoftware.com>.

David Gallagher
CAChe Group, Fujitsu
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