From chemistry-request@server.ccl.net Mon Jul 22 21:08:11 2002 Received: from web12806.mail.yahoo.com ([216.136.174.41]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6N18Br00897 for ; Mon, 22 Jul 2002 21:08:11 -0400 Message-ID: <20020723010810.83438.qmail@web12806.mail.yahoo.com> Received: from [61.9.73.249] by web12806.mail.yahoo.com via HTTP; Mon, 22 Jul 2002 18:08:10 PDT Date: Mon, 22 Jul 2002 18:08:10 -0700 (PDT) From: amor san juan Subject: Summary: Energy minimization To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii My question posted: -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On Behalf Of amor san juan Sent: Sunday, July 21, 2002 4:09 AM To: chemistry@ccl.net Subject: CCL:Energy minimization Hello, What are the good minimization algorithms for up to 150max atoms? My goal to this most stable energy conformer is to use it in docking experiment. I tried MM3 & MMFF94 algorithms built in a specific commercial software. Results showed that none of the minimized structures in synchronized with ben.pdbq distributed file in AutoDock. Im calling the attention of Autodock users, have you encountered this problem? Kindly give me a hint. I would also appreciate if someone would be considerate to give me good reading materials about energy minimization. Thanks, Amor ************************************ Hi amor san juan, I think I have suggestion for your energy minimization problem. With my experience with MM3, more than 90-100 atoms will give you a realiable structures but you really need to be very careful with the energies. I don't know which version of the MM programs you have, but in the original Allinger's program it is an option called "Stochastic Search" where you ramdomly move the atoms in the space and then minimize the energy. As a result, you can do conformational search all around the energy surphase avoiding the problem of the local minima. I have been using this option for molecules with 80-100 atoms at works very well. Once again let me tell you that the energy values of this programs are very questionable when it is applied to more than 100 atoms. If you are interested in the energies I rather will use something like semi-empirical calculation (AM1, PM3, etc). I hope this is will help you. Jorge Gonzalez -- Jorge Gonzalez Outeirino Complex Carbohydrate Research Center University of Georgia 220 Riverbend Road 30602 Athens Georgia USA e-mail: uccajgo7@netscape.net Amor, EM will never synchronize with a crystal structure! Its just a theoretical adjustment of bonds and angles, and is used for refining models, and region with High B-factor. Quick summary of EM: Steepest descent; refining, requires youto be in or close to a local minimum. Conjugate Gradient: "rough" structure alternations, to rock a model hopefully in a better local minimum. Extensive reading : Leach A. (2001). Molecular Modelling: Principles and applications. 2nd Ed. Pearson Education Limited. Good luck! Sergio Good reading material, well Leach "Molecular Modelling" and Jenssen "Introduction to Computational Chemistry" are quite good. Mr James J Robinson MRSC Molecular Modeller Pharmacy and Pharmacology Dept. University of Bath Claverton Down Bath, Somerset, UK. BA2 7AY. J.J.Robinson@bath.ac.uk http://www.bath.ac.uk tel +44(0) 1225 384723 MM3 and MMFF94 are not minimization algorithms but force fields, i.e. they yield the energy of a given system. Your commercial program used a minimization algorithm (e.g. steepest descent, conjugate gradients, BFGS, EF) to minimize the energy (force field function) with respect to the coordinates. Thus, an answer to your question is twofold: 1, energy function You can use a force field (cheap); the rather small size of your system also would allow you to choose semiempirical MO methods, in order to take care of polarization effects. 2, minimization Because your system is that small, you should use a quasi-Newton method, like BFGS or EigenvectorFollwing. One could also think of molecular dynamics or Monte Carlo (simulated annealing) - but this depends strongly on the resources you have and the your intentions. Regards, Anselm __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.yahoo.com From chemistry-request@server.ccl.net Mon Jul 22 10:16:21 2002 Received: from seraph2.grc.nasa.gov ([128.156.10.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6MEGL323105 for ; Mon, 22 Jul 2002 10:16:21 -0400 Received: from lombok-fi.lerc.nasa.gov (lombok-fi.lerc.nasa.gov [139.88.112.33]) by seraph2.grc.nasa.gov (Postfix) with ESMTP id 4374DC6903 for ; Mon, 22 Jul 2002 10:16:16 -0400 (EDT) Received: from apataki-fi.lerc.nasa.gov (apataki-fi.lerc.nasa.gov [139.88.112.35]) by lombok-fi.lerc.nasa.gov (NASA GRC 8.12.3/8.12.3) with ESMTP id g6MEGFBg010709; Mon, 22 Jul 2002 10:16:15 -0400 (EDT) Received: from mzehe.grc.nasa.gov (mzehe.lerc.nasa.gov [139.88.15.36]) by apataki-fi.lerc.nasa.gov with ESMTP (8.8.8+Sun/2.20-grc) id KAA24888; Mon, 22 Jul 2002 10:16:14 -0400 (EDT) Message-Id: <5.1.0.14.2.20020722095110.00a6c040@popserve.grc.nasa.gov> X-Sender: mszehe@popserve.grc.nasa.gov X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Mon, 22 Jul 2002 10:15:45 -0400 To: "Bill Smith" From: Michael J Zehe Subject: Re: CCL:Equilibrium constants Cc: chemistry@ccl.net In-Reply-To: <3D394C93.2969.35AB18B@localhost> References: <3D38AB58.453C1A18@georgetown.edu> Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_239877603==_.ALT" --=====================_239877603==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed A convenient source of up-to-date thermodynamic data in an easily-used form is the program PFC, at http://cea.grc.nasa.gov/. PFC allows the user to get accurate data for over 2000 species contained in the NASA Glenn (formerly NASA Lewis) database, documented in NASA TP-2002-211556 and at http://www.grc.nasa.gov/www/ceaweb . This database has been maintained and documented for almost 50 years by Ms. Bonnie Mcbride et al at NASA Glenn in support of the NASA chemical equilibrium progam CEA. .At 11:42 AM 07/20/2002 -0400, Bill Smith wrote: >Apart from standard tables like the JANAF Tables (CHASE, M., Jr., 1998, >{\it NIST-JANAF Thermochemical Tables, 4th ed., J. Phys. and Chem. >Reference Data Monograph No. 9,} (Am.Chem. Society, Am. Inst. >Physics).Data , you can get a lot of this data from the free Lite version >of the reaction equilibrium software package EQS4WIN, available at > >http://www.mathtrek.com > > >On 19 Jul 2002, at 20:14, knauerc wrote: > > > Does anyone know where I can find good data for the equilibrium > > constants, (as a function of temperature), for the reactions: > > > > H2 + Cl2 = 2HCL > > > > and > > > > H2 + Br2 = 2HBr > > > > Thank you. > > > > Connie Knauer > > Georgetown University > > knauerc@georgetown.edu > > > > > > > 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 > > > > > > > > > > > > > >-= 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 > > > > > > Michael J. Zehe (216) 433-5833 --=====================_239877603==_.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable A convenient source of up-to-date thermodynamic data in an easily-used form is the program PFC, at http://cea.grc.nasa.= gov/. 
PFC allows the user to get accurate data for over 2000 species contained in the NASA Glenn (formerly NASA Lewis) database, documented in
NASA TP-2002-211556  and at  http://www= .grc.nasa.gov/www/ceaweb . This database has been maintained and documented for almost 50 years by=
Ms. Bonnie Mcbride et al at NASA Glenn in support of the NASA chemical= equilibrium progam CEA.




.At 11:42 AM 07/20/2002 -0400, Bill Smith wrote:
Apart from standard tables like the= JANAF Tables (CHASE, M., Jr., 1998, {\it NIST-JANAF Thermochemical Tables,= 4th ed., J. Phys. and Chem. Reference Data Monograph No. 9,} (Am.Chem.= Society, Am. Inst. Physics).Data , you can get a lot of this data from the free Lite= version of the reaction equilibrium software package EQS4WIN, available at=

http://www.mathtrek.com


On 19 Jul 2002, at 20:14, knauerc wrote:

> Does= anyone know where I can find good data for the equilibrium
> constants, (as a function of temperature), for the reactions:
>
> H2 + Cl2 =3D 2HCL
>
> and
>
> H2 + Br2 =3D 2HBr
>
> Thank you.
>
> Connie Knauer
> Georgetown University
> knauerc@georgetown.edu
>
>

> CHEMISTRY@ccl.net -- To Everybody  | CHEMISTRY-REQUEST@ccl.net --= To
> Admins Ftp: ftp.ccl.net |  WWW: http://www.ccl.net/chemistry/&nb= sp;  |
> Jan: jkl@ccl.net
>
>
>
>





-=3D This is automatically added to each message by mailing script =3D-= CHEMISTRY@ccl.net -- To Everybody  | CHEMISTRY-REQUEST@ccl.net -- To= Admins Ftp: ftp.ccl.ne= t |  WWW: http://www.ccl.net/chemistry/&nb= sp;  | Jan: jkl@ccl.net





</blockquote></x-html>


Michael J. Zehe
(216) 433-5833 --=====================_239877603==_.ALT-- From chemistry-request@server.ccl.net Mon Jul 22 10:16:52 2002 Received: from mail.fqspl.com.pl ([212.244.147.20]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6MEGn323179 for ; Mon, 22 Jul 2002 10:16:51 -0400 Received: (qmail 28882 invoked from network); 22 Jul 2002 14:24:56 -0000 Received: from unknown (HELO JAREK) (212.244.147.4) by mail.fqspl.com.pl with SMTP; 22 Jul 2002 14:24:56 -0000 Message-ID: <191901c2318b$2089c470$270a0a0a@JAREK> Reply-To: "Jaroslaw Pawlak" From: "Jaroslaw Pawlak" To: Subject: BioAdviser 1.0 Date: Mon, 22 Jul 2002 16:20:42 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-2" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 FQS Poland is pleased to announce the release of BioAdviser 1.0. BioAdviser 1.0 is super-fast software for displaying, analysing, and manipulating 3-D structures of biological macromolecules, with special emphasis on the study of proteins and enzymes. It also delivers superb tools for analysis of smaller molecules. To learn more, please visit: http://www.fqspl.com.pl/bioadviser Best regards, FQS Poland Team ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FQS Poland Palac Pugetow; ul. Starowislna 13-15 31-038 Krakow, Poland Tel.: (+48 12) 429 43 45 Fax: (+48 12) 429 61 24 e-mail: ccs@fqspl.com.pl URL: http://www.fqspl.com.pl From chemistry-request@server.ccl.net Mon Jul 22 11:12:50 2002 Received: from so.sd.lionbioscience.com ([209.68.255.43]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6MFCn324722 for ; Mon, 22 Jul 2002 11:12:50 -0400 Received: from tempest.sd.lionbioscience.com (tempest.sd.lionbioscience.com [10.8.0.8]) by so.sd.lionbioscience.com (8.11.3/8.11.3) with ESMTP id g6MFCIg28924; Mon, 22 Jul 2002 08:12:19 -0700 (PDT) Received: by tempest.sd.lionbioscience.com with Internet Mail Service (5.5.2653.19) id ; Mon, 22 Jul 2002 08:12:07 -0700 Message-ID: From: Stephen Bowlus To: "'Jianquan Chen'" , chemistry@ccl.net Subject: RE: summary on adding charges to thousands of molecule via MOPAC Date: Mon, 22 Jul 2002 08:12:04 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C23192.230C9A90" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C23192.230C9A90 Content-Type: text/plain; charset="iso-8859-1" Charges from Huckel and extended Huckel theory rely only on the connectivity of the system. To the extent that Gasteiger charges (and its several variants) are elaborations of Huckel theory, I would expect these would give reliable charges, within the framework of that theory. In fact, adding Gasteiger-Huckel charges to a 2D molecule (MDL sdf files) before optimizing the molecule in Sybyl (using a force field, which captures the connectivity information) is a fairly common task in our lab. You can do these calculations in Alchemy (cheap) or VEGA (free!). You might also check TINKER (as a free/cheapware), but I am not experienced in its use. Doing 1SCF in MOPAC on a 2D molecule will give you meaningless charges (not just inaccurate!). This is because MOPAC's (NDO) methods do not depend on the "bonding" information implied by a connection table - bonding is inferred after a stable (optimized) configuration of the nuclei in the electron soup is calculated. The charges will be calculated (you can always do the calculation!) but the 2D molecule is so far from a stable configuration that heaven alone knows what they will mean. "Inflating" a 2D molecule to 3D in MOPAC _may_ work, but again, since bonding is inferred after optimization, there is a good chance that your structures will be ... ummm, novel? This is particularly true if you start with Cartesian coordinates. With the Z-matrix (internal coordinates) ... maybe yes, maybe not. I've had some wonderful experiences with poorly defined (in 3-space) starting structures giving very strange molecules after optimization when I drew in the lines representing what I thought were bonds. At best, you will need to carefully review each structure after the calculation. Hope this helps, Steve ------_=_NextPart_001_01C23192.230C9A90 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable RE: summary on adding charges to thousands of molecule via = MOPAC

Charges from Huckel and extended Huckel theory rely = only on the connectivity of the system.  To the extent that = Gasteiger charges (and its several variants) are elaborations of Huckel = theory, I would expect these would give reliable charges, within the = framework of that theory.  In fact, adding Gasteiger-Huckel = charges to a 2D molecule (MDL sdf files) before optimizing the molecule = in Sybyl (using a force field, which captures the connectivity = information) is a fairly common task in our lab.  You can do these = calculations in Alchemy (cheap) or VEGA (free!).  You might also = check TINKER (as a free/cheapware), but I am not experienced in its = use.

Doing 1SCF in MOPAC on a 2D molecule will give you = meaningless charges (not just inaccurate!).  This is because = MOPAC's (NDO) methods do not depend on the "bonding" = information implied by a connection table - bonding is inferred after a = stable (optimized) configuration of the nuclei in the electron soup is = calculated.  The charges will be calculated (you can always do the = calculation!) but the 2D molecule is so far from a stable configuration = that heaven alone knows what they will mean.

"Inflating" a 2D molecule to 3D in MOPAC = _may_ work, but again, since bonding is inferred after optimization, = there is a good chance that your structures will be ... ummm, = novel?  This is particularly true if you start with Cartesian = coordinates.  With the Z-matrix (internal coordinates) ... maybe = yes, maybe not.  I've had some wonderful experiences with poorly = defined (in 3-space) starting structures giving very strange molecules = after optimization when I drew in the lines representing what I thought = were bonds.  At best, you will need to carefully review each = structure after the calculation.

Hope this helps,
Steve

------_=_NextPart_001_01C23192.230C9A90-- From chemistry-request@server.ccl.net Mon Jul 22 08:53:34 2002 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6MCrX320376 for ; Mon, 22 Jul 2002 08:53:34 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id IAA00010; Mon, 22 Jul 2002 08:53:34 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Mon, 22 Jul 2002 08:51:35 -0400 Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GZN000JZI6YJ9@lvlmail.unitedcatalysts.com>; Mon, 22 Jul 2002 08:47:22 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2653.19) id <3VB0MNT4>; Mon, 22 Jul 2002 08:50:42 -0400 Content-return: allowed Date: Mon, 22 Jul 2002 08:50:42 -0400 From: "Shobe, Dave" Subject: RE: Equilibrium constants To: "'knauerc'" , chemistry@ccl.net Message-id: <157A51F55AAAD3119CD70008C7B1629D01C15EC2@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g6MCrY320377 The NIST WebBook (http://webbook.nist.gov/chemistry/) has thermochemical data as a function of temperature, and you can calculate equilibrium constants in the usual way. --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: knauerc [mailto:knauerc@georgetown.edu] Sent: Friday, July 19, 2002 8:14 PM To: chemistry@ccl.net Subject: CCL:Equilibrium constants Does anyone know where I can find good data for the equilibrium constants, (as a function of temperature), for the reactions: H2 + Cl2 = 2HCL and H2 + Br2 = 2HBr Thank you. Connie Knauer Georgetown University knauerc@georgetown.edu -= 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 Mon Jul 22 08:04:05 2002 Received: from mailhub.health.nb.ca ([207.179.181.34]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6MC44319089 for ; Mon, 22 Jul 2002 08:04:05 -0400 Received: from onco_irmb.health.nb.ca ([10.10.100.12]) by mailhub.health.nb.ca (Post.Office MTA v3.5.3 release 223 ID# 607-57574U3000L300S0V35) with ESMTP id ca for ; Mon, 22 Jul 2002 09:03:59 -0300 Message-Id: <5.1.1.6.0.20020722085737.00a04a00@mailhub.health.nb.ca> X-Sender: miroslavac@mailhub.health.nb.ca X-Mailer: QUALCOMM Windows Eudora Version 5.1.1 Date: Mon, 22 Jul 2002 09:03:58 -0300 To: CCL From: miroslavac@health.nb.ca (Miroslava Cuperlovic-Culf) Subject: Summary: isoelectric pointi Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_182102318==.ALT" --=====================_182102318==.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Dear All, recently I posted a question: > I am looking for (ideally free) software that can calculate local > isoelectric point (pI) for amino acids in a relatively large protein > (~40kDa). Also I would appreciate information about references dealing with > calculation of reactivity of cysteine residues in proteins. I am very grateful to few people that send me replies (thanks to: Julien Michel, Guilherme, Sergio Manzetti). Suggestions were to look at two free programs: - ProtParam at www.expasy.org (where I found many other useful programs) - prof. Bashford's MEAD (Macroscopic Eletrostatics with Atomic Detail) program http://www.scripps.edu/bashford/ (which I still have a bit of a hard time ftp-ing) I didn't get any replies about references so any additional information will be appreciated. Thanks again, Mira Miroslava Cuperlovic-Culf Research Scientist Beausejour Medical Research Institute 37 Providence Street Moncton, NB E1C 8X3 Canada fax: 506-862-4222 tel: 506-862-4848 e-mail: miroslavac@health.nb.ca --=====================_182102318==.ALT Content-Type: text/html; charset="us-ascii" Dear All,
recently I posted a question:

> I am looking for (ideally free) software that can calculate local
> isoelectric point (pI) for amino acids in a relatively large protein
> (~40kDa). Also I would appreciate information about references dealing with
> calculation of reactivity of cysteine residues in proteins.

I am very grateful to few people that send me replies (thanks to: Julien Michel, Guilherme, Sergio Manzetti).

Suggestions were to look at two free programs:
- ProtParam at www.expasy.org (where I found many other useful programs)
- prof. Bashford's MEAD (Macroscopic Eletrostatics with Atomic Detail) program http://www.scripps.edu/bashford/ (which I still have a bit of a hard time ftp-ing)


I didn't get any replies about references so any additional information will be appreciated.
Thanks again,
Mira


Miroslava Cuperlovic-Culf
Research Scientist
Beausejour Medical Research Institute
37 Providence Street
Moncton, NB E1C 8X3
Canada
fax: 506-862-4222
tel: 506-862-4848
e-mail: miroslavac@health.nb.ca
--=====================_182102318==.ALT-- From chemistry-request@server.ccl.net Tue Jul 23 15:46:11 2002 Received: from hotmail.com ([64.4.15.95]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6NJkAr30834 for ; Tue, 23 Jul 2002 15:46:11 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Tue, 23 Jul 2002 12:46:05 -0700 Received: from 128.235.242.51 by lw10fd.law10.hotmail.msn.com with HTTP; Tue, 23 Jul 2002 19:46:05 GMT X-Originating-IP: [128.235.242.51] From: "Deepangi Pandit" To: chemistry@ccl.net Subject: pdbqs and pdbq in AUTODOCk 3.0.5 Date: Tue, 23 Jul 2002 15:46:05 -0400 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 23 Jul 2002 19:46:05.0734 (UTC) FILETIME=[9554FC60:01C23281] Hello Everybody: I have a question regarding formats of macromolecule file, which we have to covert from one format to another while performing docking using AutoDock. Please be free to correct me if I am wrong but as far as I understand macromolecule in pdbq file is with is with partial charge and in pdbqs it is with solvation parameters for macromolecule but I do not understand one thing that when I observe pdbqs using SYBYL why pdbqs has amino acids in the form: - Glu83 Glu83 Glu83 Glu83- Glu 83- Glu 83- Glu 83 Val84 Val84 Val84 Val84- Val84- Val84- Val84 and so on..... Thank you very much for your time. Deepangi _________________________________________________________________ Send and receive Hotmail on your mobile device: http://mobile.msn.com From chemistry-request@server.ccl.net Tue Jul 23 12:01:49 2002 Received: from mail.csusb.edu ([139.182.2.16]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6NG1mr23719 for ; Tue, 23 Jul 2002 12:01:48 -0400 Received: from Debug (mail.csusb.edu [139.182.2.16]) by mail.csusb.edu (8.12.5/8.12.5) with SMTP id g6NG095j026696 for ; Tue, 23 Jul 2002 09:00:09 -0700 (PDT) Message-Id: <200207231600.g6NG095j026696@mail.csusb.edu> To: CCL From: kcousins@csusb.edu Subject: summary: MacBabel Date: Tue, 23 Jul 2002 09:00:09 US/Pacific X-Mailer: Endymion MailMan Standard Edition v3.0.20 Thanks to those who replied. ******** My original question: Has anyone been able to get Babel for mac to work on a G3/G4 with System 9.x? I used to use this a while back, but now just get errors with either the with or without fpu code (won't execute). I'm using the only versions I can find; macbabel 1.3. ********** The answer (thanks to several individuals whose identities are lost in my deleted mail files) OpenBabel will (should?) work at the Mac OS X (10.x) command line. See http://openbabel.sourceforge.net/ for more information. ************* There appears to be no other solution for Mac OS 9.x and G3/G4 computers that to upgrade to OS x. Kimberley Cousins Associate Professor of Chemistry California State University, San Bernardino 5500 University Parkway San Bernardino, CA 92407 (909)880-5391 kcousins@csusb.edu http://chem.csusb.edu/~kcousins From chemistry-request@server.ccl.net Tue Jul 23 17:11:49 2002 Received: from deluge.cc.mcgill.ca ([132.206.27.50]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6NLBnr00854 for ; Tue, 23 Jul 2002 17:11:49 -0400 Received: from dna.mcgill.ca (dna.McGill.CA [132.206.27.48]) by deluge.cc.mcgill.ca (8.12.3/8.11.0) with ESMTP id g6NLBir1004025 for ; Tue, 23 Jul 2002 17:11:48 -0400 (EDT) Received: from mcgill (ariya3.Chem.McGill.CA [132.206.175.121]) by dna.mcgill.ca (8.12.2/8.12.0) with ESMTP id g6NLBaoo012006 for ; Tue, 23 Jul 2002 17:11:44 -0400 (EDT) From: "Alexei Khalizov" To: chemistry@ccl.net Date: Tue, 23 Jul 2002 17:11:36 -0400 MIME-Version: 1.0 Subject: A problem with O(1D) Reply-to: alexei.khalizov@mcgill.ca Message-ID: <3D3D8E3C.28301.4E99E562@localhost> Priority: normal X-mailer: Pegasus Mail for Windows (v4.01) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Content-description: Mail message body Dear CCLers, Does anyone know how to calculate correctly the energy of an oxygen atom in the singlet state O(1D)? I am having a problem of evaluating the singlet-triplet energy difference E(S-T) = E[O(1D)] - E[O(3P)] whose experimental value is 190 kJ/mol. Using DFT methods (B3LYP and PW91) with small basis sets (6-31G*) significantly overestimates this energy splitting, giving E(S-T) = 270-280 kJ/mol. Calculation at CCSD(T)/6-311+G(3df) level of theory leads to a better result, however, it is still far from being acceptable, E(S-T) = 214 kJ/mol. So far I have found that it is the energy of O(1D) that is incorrect while the energy of O(3P) is reproduced properly. What goes wrong? The wavefunction for O(1D) seems to be correct - population analysis shows that it is symmetrical (2Px alpha) (2Px beta) (2Py alpha) (2Py beta). Thank you in advance, Alexei ------------------------- Dr. Alexei Khalizov Department of Chemistry McGill University, 801 Sherbrooke St. W., Montreal, Quebec, CANADA, H3A 2K6 Phone: (514) 398-6920 Fax: (514) 398-2382 From chemistry-request@server.ccl.net Tue Jul 23 21:20:34 2002 Received: (from ccl@localhost) by server.ccl.net (8.11.6/8.11.0) id g6O1KYw18578 for chemistry@ccl.net; Tue, 23 Jul 2002 21:20:34 -0400 Message-Id: <200207240120.g6O1KYw18578@server.ccl.net> Date: Tue, 23 Jul 2002 18:28:22 -0500 Subject: 02.09.20 Vanderbilt Biomolecular Modeling Symposium, Nashville, TN From: Terry P Lybrand To: chemistry@ccl.net Vanderbilt Biomolecular Modeling Symposium September 20 and 21, 2002 Vanderbilt University will host a symposium on biomolecular modeling techniques and applications on September 20 and 21. Registration for the symposium is free, but slots are limited, so early registration is recommended. For detailed information on the program, accommodations, and on-line registration, please see: http://structbio.vanderbilt.edu/comp/symposium/ ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dr. Terry P. Lybrand, Ph.D. Professor of Chemistry Center for Structural Biology 5154C Biosci/MRB III e-mail: terry.p.lybrand@vanderbilt.edu Tel: (615)-343-1247 Fax: (615)-936-2211 U.S. Mail Vanderbilt University Center for Structural Biology 5142 Biosci/MRB III Nashville, TN 37232-8725 From chemistry-request@server.ccl.net Tue Jul 23 18:13:29 2002 Received: from localhost.localdomain ([148.122.30.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6NMDRr02366 for ; Tue, 23 Jul 2002 18:13:28 -0400 Received: from localhost (localhost [[UNIX: localhost]]) by localhost.localdomain (8.11.6/8.11.6) id g6NME1k08450 for chemistry@ccl.net; Wed, 24 Jul 2002 00:14:01 +0200 Content-Type: text/plain; charset="us-ascii" From: Sergio To: CCL Subject: Swiss PDB Viewer in Red Hat 7.3 Date: Wed, 24 Jul 2002 00:14:00 +0200 User-Agent: KMail/1.4.1 MIME-Version: 1.0 Message-Id: <200207240014.00900.sergio@proinformatix.com> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g6NMDTr02367 Hi, has anyone managed to install SPDBV in Red Hat 7.3 in redirect the old Mesa library to the new OpenGL library? I haven't... Anyone has, please let me know! Sergio From chemistry-request@server.ccl.net Tue Jul 23 17:44:45 2002 Received: from chemdept.chem.ou.edu ([129.15.12.110]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6NLijr01643 for ; Tue, 23 Jul 2002 17:44:45 -0400 Received: from [129.15.12.142] (HELO HPC102.chemdept.chem.ou.edu) by chemdept.chem.ou.edu (Stalker SMTP Server 1.8b8) with ESMTP id S.0000081876 for ; Tue, 23 Jul 2002 16:24:30 -0500 Message-Id: <5.1.0.14.0.20020723160438.0200cdd0@chemdept.chem.ou.edu> X-Sender: sboesch@chemdept.chem.ou.edu X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Tue, 23 Jul 2002 16:22:13 -0500 To: chemistry@ccl.net From: "Scott E. Boesch" Subject: Compiling GAMESS + CHARMM on Linux Cluster Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hello All, Has anyone been able to compile CHARMM with GAMESS on a Linux cluster? We recently acquired CHARMM (c28b2). It compiles fine on the cluster (the GNU compiler was used). The newest version of GAMESS-US was obtained (Jun 2002). The installation instructions for compiling GAMESS in CHARMM were followed and then I tried to compile this--however, no success. The last two lines of the logfile for the build are collect2: ld returned 1 exit status make: *** [/usr/local/charmm_gamess-us/c28b2/exec/gnu/charmm] Error 1 Has this happened to anyone else? Thanks for any advice or suggestions. Regards, Scott Scott E. Boesch Voice: 405-325-5159 Department of Chemistry Fax: 405-325-6111 University of Oklahoma