From chemistry-request@server.ccl.net Sat Feb 15 16:05:10 2003 Received: from ns0.scripps.edu ([192.42.82.58]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1FL59x30519 for ; Sat, 15 Feb 2003 16:05:10 -0500 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns0.scripps.edu (8.11.6/TSRI-4.1rx) with SMTP id h1FL5A822045 for ; Sat, 15 Feb 2003 13:05:10 -0800 (PST) Received: from relay2.scripps.edu(137.131.200.30) by antigen.scripps.edu via csmap id 9698; Sat, 15 Feb 2003 12:57:52 -0800 (PST) Received: from gage.scripps.edu (gage.scripps.edu [137.131.252.115]) by relay2.scripps.edu (8.11.6/TSRI-4.2rAV) with ESMTP id h1FL4sC29413; Sat, 15 Feb 2003 13:04:54 -0800 (PST) Received: from gage (localhost [127.0.0.1]) by gage.scripps.edu (8.9.2/TSRI-3.0.1) with ESMTP id MAA10145; Sat, 15 Feb 2003 12:37:46 -0800 (PST) Message-Id: <200302152037.MAA10145@gage.scripps.edu> To: "CUI, Guanglei" , chemistry@ccl.net Cc: bashford@scripps.edu Subject: Re: CCL:MEAD pKa calculations In-Reply-To: Your message of "Thu, 13 Feb 2003 23:29:23 EST." Date: Sat, 15 Feb 2003 12:37:46 -0800 From: Don Bashford >>>>> "CUI" == CUI, Guanglei writes: > Don> My guess is it [the choice of which lysine H to zero] won't > Don> make so much difference, but why not try > Don> it all three ways? CUI> One of the three is different from the other two. pkint is CUI> calculated around 8. Very interesting ... CUI> UNK is triclosan. It's neutral. The phenol hydroxyl hydrogen CUI> is hydrogen-bonded to the TYR in hydrogen-added crystal CUI> structure. The LYS is the only titratable group sticking CUI> inside of the protein. From the great impact of hydrogen CUI> atoms of the LYS, I guess the same effect could happen to UNK CUI> too. Okay, my guess (that which H is zeroed doesn't matter) was wrong. It sounds like you have potential H-bonding networks involving the ionizable residues that can have important energetic consequences. That means, at a minimum, at all protonation microstates, you should take care to have hydrogen positions that are optimal in terms of H-bonding networks. A more rigorous approach is to do calculations allowing for multiple possible H-positions, and proper statistical averaging which allows for the correnct arrangements to predominate. Neither of these things is automatic in MEAD. You need to look carefully at the structure, perhaps using molecular mechanics programs to search for and try out various H-bond arrangments, etc. For some examples of how we've handled such situations, have a look at Demchuk et al, Biochem 39:1100 (2000); and Spassov et al, JMB 312:203, (2001). In particular, see the Demchuk paper for how we handle charge parameters for a phenolate group; if a buried negative phenol is a real possibility, then delocalization of the negative charge is going to be an important issue. CUI> Here's the .g file. All terms are fairly small... CUI> 1 1 0.000000e+00 CUI> 1 2 2.158370e-02 CUI> 1 3 4.047996e-02 CUI> 2 1 2.158370e-02 CUI> 2 2 0.000000e+00 CUI> 2 3 2.034296e-02 CUI> 3 1 4.047996e-02 CUI> 3 2 2.034296e-02 CUI> 3 3 0.000000e+00 Actually, those are not small at all! The energy units are your input charge units squared divided by your imput length units, so typically protons**2/Ang. The conversion factor to pK units is about 250, or to kcal/mole, about 330. So, for example the interaction between sites 1 and 3 is worth about 10 pK units! Cheers, Don From chemistry-request@server.ccl.net Fri Feb 14 13:43:11 2003 Received: from tigre ([158.109.14.43]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1EIhAx26809 for ; Fri, 14 Feb 2003 13:43:11 -0500 Received: from gali by tigre with local (Exim 3.35 #1 (Debian)) id 18jkkW-0006Au-00 for ; Fri, 14 Feb 2003 19:39:48 +0100 Date: Fri, 14 Feb 2003 19:39:48 +0100 From: Gali Drudis Sole To: chemistry@ccl.net Subject: Re: CCL:Temperature monitoring under Linux Message-ID: <20030214183948.GA23404@tigre.qf.uab.es> Mail-Followup-To: chemistry@ccl.net References: Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Disposition: inline Content-Transfer-Encoding: 8bit In-Reply-To: User-Agent: Mutt/1.3.28i Sender: Debian User > found them to be quite heat-sensitive. We would therefore like to monitor > component temperature in them (ideally selectively for CPU, memory etc.) > What kind of approaches - both hardware and software - have people found > to be effective for this goal? Most new computers come with built-in temperature sensors as well as voltage sensors or fan speed sensors. Therefore you will probably only need the software to read it. You will have to download and compile the kernel modules you will find in: http://secure.netroedge.com/~lm78/index.html If you are using Debian there is a package (lm-sensors-source) which has all you need to build the modules. I have been using them with kernel 2.4.17 and Debian to avoid burning the CPU if a fan stopped. I can send you the scripts if you need them. Best regards, -- Galí Drudis i Solé gali@klingon.uab.es Edifici Cn., Unitat Química Física Universitat Autònoma de Barcelona, 08193 - Bellaterra, Catalonia Unitat de Química Física Tel: +34 93-581.28.57 Fax: 581.29.20 Unitat de Química Orgànica Tel: +34 93-581.17.10 Fax: 581.12.65 From chemistry-request@server.ccl.net Fri Feb 14 15:59:50 2003 Received: from noturus.usu.edu ([129.123.1.198]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1EKxnx29789 for ; Fri, 14 Feb 2003 15:59:49 -0500 Received: from pc3 (pc3.chem.usu.edu [129.123.3.37]) by noturus.usu.edu (8.11.6/8.11.6) with SMTP id h1EKqxW30560; Fri, 14 Feb 2003 13:52:59 -0700 Reply-To: From: "Tapas Kar" To: "Dr. Daniel Glossman-Mitnik" , Subject: RE: software for plotting spectra Date: Fri, 14 Feb 2003 13:50:27 -0700 Message-ID: MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0021_01C2D430.08010B00" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) In-reply-to: <002f01c2d3dc$11a53220$ed94fea9@cimav.edu.mx> X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Importance: Normal X-MailScanner: Found to be clean This is a multi-part message in MIME format. ------=_NextPart_000_0021_01C2D430.08010B00 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit For IR spectra Please contact Dr.Xiaofeng Frank Duan (duanx@asc.hpc.mil ) at WPAFB, Ohio. and for UV-Vis S. I. Gorelsky [gorelsky@stanford.edu]. Good Luck *********************************************** "We owe a lot to the Indians, who taught us how to count, without which no worthwhile scientific discovery could have been made." - Albert Einstein - ---------------------------------------------------------------------------- ---- Tapas Kar, Ph. D Department of Chemistry & Biochemistry Utah State University Logan, UT 84322-0300 Tel: 435-797-7230 Fax: 435-797-3390 Email: tapaskar@cc.usu.edu Web:http://www.chem.usu.edu/faculty/Tapas/index.html -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On Behalf Of Dr. Daniel Glossman-Mitnik Sent: Thursday, February 13, 2003 8:49 PM To: chemistry@ccl.net Subject: CCL:software for plotting spectra Dear netters: Can you point me to Windows programs that take the frequency output from Gaussian98 and render a drawing of the actual IR spectra (i.e. fitted to Gaussians or Lorentzians) ? And the same for ZINDO outputs that render the actual UV-Vis spectra ? Thanks in advance Dr. Daniel Glossman-Mitnik ********************************************************************** Dr. Daniel Glossman-Mitnik CIMAV - Centro de Investigacion en Materiales Avanzados LAQUICOM - Laboratorio de Quimica Computacional Miguel de Cervantes 120 - Complejo Industrial Chihuahua Chihuahua, Chih. 31109 - Mexico Tel: (52) 614 4391151 FAX: (52) 614 4391112 E-mail: daniel.glossman@cimav.edu.mx glossman@hotmail.com dglossman@yahoo.com ********************************************************************** ------=_NextPart_000_0021_01C2D430.08010B00 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
For IR = spectra=20 Please contact Dr.Xiaofeng Frank Duan (duanx@asc.hpc.mil ) at = WPAFB, Ohio.=20
and = for UV-Vis =20 S. I. Gorelsky [gorelsky@stanford.edu].
Good=20 Luck
 

***********************************************
"We owe a lot to the Indians, who taught = us how to=20 count, without
which no worthwhile scientific discovery could have = been=20 made."
         &n= bsp;           &nb= sp;           &nbs= p;        =20 - Albert Einstein=20 -
--------------------------------------------------------------------= ------------
Tapas=20 Kar, Ph. D
Department of Chemistry & Biochemistry
Utah State=20 University
Logan, UT 84322-0300

Tel: 435-797-7230
Fax:=20 435-797-3390
Email: tapaskar@cc.usu.edu
Web:http://www.chem.usu.edu/faculty/Tapas/index.html

-----Original Message-----
From: Computational = Chemistry List=20 [mailto:chemistry-request@ccl.net]On Behalf Of Dr. Daniel=20 Glossman-Mitnik
Sent: Thursday, February 13, 2003 8:49=20 PM
To: chemistry@ccl.net
Subject: CCL:software for = plotting spectra

 

Dear netters:
 
Can you point me to Windows = programs=20 that take the frequency output from
Gaussian98 and render a = drawing of the=20 actual IR spectra (i.e. fitted to
Gaussians or Lorentzians)=20 ?
 
And the same for ZINDO = outputs that=20 render the actual UV-Vis spectra ?
 
Thanks in = advance
 
          &nbs= p;            = ;            =         =20 Dr. Daniel Glossman-Mitnik
 
****************************************************************= ******
Dr.=20 Daniel Glossman-Mitnik
CIMAV - Centro de Investigacion en = Materiales=20 Avanzados
LAQUICOM - Laboratorio de Quimica Computacional
Miguel = de=20 Cervantes 120 - Complejo Industrial Chihuahua
Chihuahua, Chih. = 31109 =20 -  Mexico
Tel: (52) 614 4391151      = FAX:=20 (52) 614 4391112
E-mail: daniel.glossman@cimav.edu.mx=
           = ;=20 glossman@hotmail.com
 &n= bsp;         =20 dglossman@yahoo.com
**********= ************************************************************
=
------=_NextPart_000_0021_01C2D430.08010B00-- From chemistry-request@server.ccl.net Fri Feb 14 13:20:16 2003 Received: from smtp2.Stanford.EDU ([171.64.14.116]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1EIKFx26279 for ; Fri, 14 Feb 2003 13:20:15 -0500 Received: from smtp2.Stanford.EDU (localhost [127.0.0.1]) by smtp2.Stanford.EDU (8.12.6/8.12.6) with ESMTP id h1EIKEVe020906 for ; Fri, 14 Feb 2003 10:20:14 -0800 (PST) Received: from SERGE (DNab407dd9.Stanford.EDU [171.64.125.217]) by smtp2.Stanford.EDU (8.12.6/8.12.6) with SMTP id h1EIKCAM020885; Fri, 14 Feb 2003 10:20:12 -0800 (PST) Message-ID: <002a01c2d455$b4ef3740$d97d40ab@SERGE> From: "S. I. Gorelsky" To: "Dr. Daniel Glossman-Mitnik" Cc: References: <002f01c2d3dc$11a53220$ed94fea9@cimav.edu.mx> Subject: Re: CCL:software for plotting spectra Date: Fri, 14 Feb 2003 10:20:08 -0800 Organization: Stanford University MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0027_01C2D412.A6440290" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1106 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 This is a multi-part message in MIME format. ------=_NextPart_000_0027_01C2D412.A6440290 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello here is one: SWizard http://www.obbligato.com/software/swizard/ Regards, S. Gorelsky ----- Original Message -----=20 From: Dr. Daniel Glossman-Mitnik=20 To: chemistry@ccl.net=20 Sent: Thursday, February 13, 2003 7:49 PM Subject: CCL:software for plotting spectra Dear netters: Can you point me to Windows programs that take the frequency output = from=20 Gaussian98 and render a drawing of the actual IR spectra (i.e. fitted = to Gaussians or Lorentzians) ? And the same for ZINDO outputs that render the actual UV-Vis spectra ? Thanks in advance Dr. Daniel Glossman-Mitnik ********************************************************************** Dr. Daniel Glossman-Mitnik CIMAV - Centro de Investigacion en Materiales Avanzados LAQUICOM - Laboratorio de Quimica Computacional Miguel de Cervantes 120 - Complejo Industrial Chihuahua Chihuahua, Chih. 31109 - Mexico Tel: (52) 614 4391151 FAX: (52) 614 4391112 E-mail: daniel.glossman@cimav.edu.mx glossman@hotmail.com dglossman@yahoo.com ********************************************************************** ------=_NextPart_000_0027_01C2D412.A6440290 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hello
here is one: SWizard http://www.obbligato.= com/software/swizard/
 
Regards,
 
S. Gorelsky
----- Original Message -----
From:=20 Dr. Daniel = Glossman-Mitnik=20
Sent: Thursday, February 13, = 2003 7:49=20 PM
Subject: CCL:software for = plotting=20 spectra

 

Dear netters:
 
Can you point me to Windows = programs=20 that take the frequency output from
Gaussian98 and render a = drawing of the=20 actual IR spectra (i.e. fitted to
Gaussians or Lorentzians)=20 ?
 
And the same for ZINDO = outputs that=20 render the actual UV-Vis spectra ?
 
Thanks in = advance
 
          &nbs= p;            = ;            =         =20 Dr. Daniel Glossman-Mitnik
 
****************************************************************= ******
Dr.=20 Daniel Glossman-Mitnik
CIMAV - Centro de Investigacion en = Materiales=20 Avanzados
LAQUICOM - Laboratorio de Quimica Computacional
Miguel = de=20 Cervantes 120 - Complejo Industrial Chihuahua
Chihuahua, Chih. = 31109 =20 -  Mexico
Tel: (52) 614 4391151      = FAX:=20 (52) 614 4391112
E-mail: daniel.glossman@cimav.edu.mx=
           = ;=20 glossman@hotmail.com
 &n= bsp;         =20 dglossman@yahoo.com
**********= ************************************************************
=
------=_NextPart_000_0027_01C2D412.A6440290-- From chemistry-request@server.ccl.net Fri Feb 14 15:30:55 2003 Received: from yakko.cimav.edu.mx ([148.223.46.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1EKUsx29251 for ; Fri, 14 Feb 2003 15:30:54 -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 h1ELLJ702172 for ; Fri, 14 Feb 2003 14:21:19 -0700 Message-ID: <001201c2d45f$f266a4f0$8400000a@LAQUICOM02> From: "Dr. Daniel Glossman-Mitnik" To: Subject: ionization potentials and electron affinities Date: Fri, 14 Feb 2003 13:33:27 -0600 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000F_01C2D42D.A7A39E50" 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_000F_01C2D42D.A7A39E50 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Dear netters: Which are the different experimental techniques that allow to obtain information about: * adiabatic ionization potentials * vertical ionization potentials * adiabatic electron affinities * vertical electron affinities ? 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 *************************************************************************= *** -------------------------------------------------------------------------= ------- =20 ------=_NextPart_000_000F_01C2D42D.A7A39E50 Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable
 
Dear netters:
 
 
Which are the different experimental techniques that allow to = obtain
information about:
 
  *  adiabatic ionization potentials
 
 *   vertical ionization potentials
 
 *  adiabatic electron affinities
 
 *  vertical electron affinities    = ?
 
 
Thanks in advance
 
           &n= bsp;           &nb= sp;       =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
**********= ******************************************************************
<= !--mail_content-->

------=_NextPart_000_000F_01C2D42D.A7A39E50-- From chemistry-request@server.ccl.net Sat Feb 15 17:32:07 2003 Received: from cascara.uvic.ca ([142.104.5.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h1FMW7x32104 for ; Sat, 15 Feb 2003 17:32:07 -0500 Received: from unix6.uvic.ca (unix6.uvic.ca [142.104.5.87]) by cascara.uvic.ca (8.12.6/8.12.6) with ESMTP id h1FMW5xC222968; Sat, 15 Feb 2003 14:32:05 -0800 Date: Sat, 15 Feb 2003 14:32:05 -0800 (PST) From: Roy Jensen To: "Dr. Daniel Glossman-Mitnik" cc: chemistry@ccl.net Subject: Re: CCL:software for plotting spectra In-Reply-To: <002f01c2d3dc$11a53220$ed94fea9@cimav.edu.mx> Message-ID: References: <002f01c2d3dc$11a53220$ed94fea9@cimav.edu.mx> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-UVic-Virus-Scanned: OK - Passed virus scan by Sophos (sophie) on cascara X-Scanned-By: MIMEDefang 2.19 (www . roaringpenguin . com / mimedefang) > Can you point me to Windows programs that take the frequency output from > Gaussian98 and render a drawing of the actual IR spectra (i.e. fitted to > Gaussians or Lorentzians) ? > > And the same for ZINDO outputs that render the actual UV-Vis spectra ? Writing a program to do this is simple (create an array that covers the range; loop through each transition and sum the (gaussian or lorentzian) intensities at each point; plot. Not optimized, but it will work. (It is even possible to get Excel to do it. I don't know why I keep touting the capabilities of Excel -- I use MathCad mostly, but get my students to use Excel for thier data analysis. No, I am not sponsored by Microsoft.) This works when you have only a few to do since you have to manually extract the band center and intensity. HOWEVER, especially for IR spectra in condensed matter, the assumption that each transition has the same width is very poor. H-bonded IR stretches are VERY broad while CN stretches are very narrow. More generally, the coupling (and variability thereof) between the atoms involved in the transition and their surroundings dictates the breadth of the transition. Roy Jensen -----BEGIN PGP PUBLIC KEY BLOCK----- Comment: available at www.consol.ca ------END PGP PUBLIC KEY BLOCK------