From chemistry-request@ccl.net Wed Aug 6 03:58:52 2003 Received: from soul.helsinki.fi (soul.helsinki.fi [128.214.3.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h767wpNG007339 for ; Wed, 6 Aug 2003 03:58:52 -0400 Received: from localhost (mpjohans@localhost) by soul.helsinki.fi (8.9.3p2/8.9.3) with ESMTP id KAA12010; Wed, 6 Aug 2003 10:58:49 +0300 (EEST) X-Authentication-Warning: soul.helsinki.fi: mpjohans owned process doing -bs Date: Wed, 6 Aug 2003 10:58:49 +0300 (EEST) From: Mikael Johansson X-X-Sender: mpjohans-.at.-soul.helsinki.fi To: Emad Tajkhorshid cc: computational Chemistry List Subject: Re: CCL:Heme charges In-Reply-To: Message-ID: References: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello Emad and All! On Tue, 5 Aug 2003, Emad Tajkhorshid wrote: > We just optimized the geometry of a porphyrin ring using DFT and > calculated ESP charges for the molecule. The iron carries a significant > amoount of positive charge according to population analyses done on the > system (it is formally 2+), but the ESP charge for it is negative! The > iron atom is completely burried inside the molecule, and that may be one > reason of getting this strange result. Has anybody else had similar > problems? Any comments, references, or suggestions are > appreciated. I had the same "problem" when trying to calculate ESP charges for a six-coordinated haem. I assume your system is also six-coordinated? As pointed out by Konrad Hinsen, this is an effect of not probing the ESP near the iron, which in practice is impossible. Your ligating N's are probably slightly too positive instead, and to the outside observers, i.e. the fitting points, it makes no difference. Depending on what you plan to use the charges for, it might make no difference for you either. The idea of fixing the iron charge was quite good, thanks Konrad! For a brief discussion on the iron charge in haems, you could look at Biochim. Biophys. Acta - Bioenergetics, 1553 (2002) 183-187. Have a nice day, Mikael J. http://www.helsinki.fi/~mpjohans/ From chemistry-request@ccl.net Wed Aug 6 11:41:26 2003 Received: from mailer.gwdg.de (mailer.gwdg.de [134.76.10.26]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h76FfQNG014329 for ; Wed, 6 Aug 2003 11:41:26 -0400 Received: from vrlab03.mpibpc.gwdg.de ([134.76.211.99] helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtp (Exim 4.20) id 19kQPh-0002bz-C7; Wed, 06 Aug 2003 17:41:21 +0200 Message-ID: <3F312187.2020809[at]mpi-bpc.mpg.de> Date: Wed, 06 Aug 2003 17:40:55 +0200 From: Vlad Cojocaru User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CCL , VMD Subject: Pressure and Gpressure output in NAMD Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Report: -0.5/6.0 ---- Start SpamAssassin results -0.50 points, 6 required; * -0.5 -- User-Agent header indicates a non-spam MUA (Mozilla) ---- End of SpamAssassin results X-Spam-Level: / X-Virus-Scanned: (clean) by exiscan+sophie Dear all, Could somebody explain me a bit the NAMD output: PRESSURE: GPRESSURE: versus the pressure and gpressure values output in the ENERGY: line? Thanks you very much, Best regards, Vlad -- Vlad Cojocaru Max Planck Institute for Biophysical Chemistry Department: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1327 e-mail: Vlad.Cojocaru[at]mpi-bpc.mpg.de home tel: ++49-551-9963204 From chemistry-request@ccl.net Wed Aug 6 13:04:57 2003 Received: from bureau6.utcc.utoronto.ca (bureau6.utcc.utoronto.ca [128.100.132.16]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h76H4vNG015526 for ; Wed, 6 Aug 2003 13:04:57 -0400 Received: from mditdell.mdit.utoronto.ca ([128.100.251.12] HELO MditDell ident: IDENT-NOT-QUERIED [port 1130]) by bureau6.utcc.utoronto.ca with SMTP id <464332-13355>; Wed, 6 Aug 2003 13:04:48 -0400 From: "William Wei" To: "CCLers" Subject: Dock5 compiling failure Date: Wed, 6 Aug 2003 13:05:50 -0500 Message-ID: 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 IMO, Build 9.0.2416 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2727.1300 Importance: Normal Dear friends, Before I post a Dock segmentation fault error. Some of you suggest that I compile it on my machine. So I tried to compile dock on my SGI machine. I used my mpi library, the version is mpich 1.2.4. I meet this error message: C++ prelinker: warning: could not locate library -loe; assuming /usr/lib/liboe.a C++ prelinker: warning: nm returned a nonzero error status ld32: FATAL 9 : I/O error (-loe): No such file or directory *** Error code 2 (bu21) Did anybody meet this problem? Do you think it is because I donot have the file liboe.a? Actually I can not find this file in my system. Any clue and suggestions is appreciated. Have a good day, William ------------------------- William Wei Faculty of Pharmacy 19 Russell Street Toronto, ON. M5S 2S2 Tel: 1-416-946-8469 Fax: 1-416-978-8511 Email: william~at~phm.utoronto.ca william.wei~at~utoronto.ca From chemistry-request@ccl.net Wed Aug 6 12:04:42 2003 Received: from wilson.acpub.duke.edu (wilson.acpub.duke.edu [152.3.233.69]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h76G4gNG014697 for ; Wed, 6 Aug 2003 12:04:42 -0400 Received: from CONCORDIA ([152.3.237.233]) by wilson.acpub.duke.edu (8.12.9/8.12.9/Duke-5.0.0) with SMTP id h76G4S0c027547; Wed, 6 Aug 2003 12:04:33 -0400 (EDT) X-Originating-IP: 152.3.169.5 X-Mailer: MyDuke.com X-Originator-Info: jz7@acpub From: To: Subject: Generalized-Mulliken-Hush method and ZINDO Date: Wed, 6 Aug 2003 11:56:33 -0400 Message-ID: <010d01c35c33$4f1a3170$eaed0398@CONCORDIA> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Thread-Index: AcNcM08a3DAeIaJASkCbN9OEblfrHw== Content-Class: urn:content-classes:message X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 Dear all, Does anyone have the experience of using Generalized-Mulliken-Hush (GMH) method and ZINDO/S (or other method to get CI results) to calculate the couppling element of photo-excited electron transfer? I got really confused about the locally-excited(LE) state and charge- transfer(CT) state. How can I find the true LE and CT states from those CI results? Really thanks a lot! Best, Jeny From chemistry-request@ccl.net Wed Aug 6 16:48:30 2003 Received: from yakko.cimav.edu.mx (yakko.cimav.ecustomer.mx [148.223.46.2] (may be forged)) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h76KmSNG019757 for >ccl.net>; Wed, 6 Aug 2003 16:48:29 -0400 Received: from yakko (localhost [127.0.0.1]) by localhost.cimav.edu.mx (Postfix) with ESMTP id 6F49A7611B for >ccl.net>; Wed, 6 Aug 2003 14:48:26 -0600 (MDT) Received: from localhost ([127.0.0.1]) by yakko.cimav.edu.mx (MailMonitor for SMTP v1.2.2 ) ; Wed, 6 Aug 2003 14:48:26 -0600 (MDT) Received: from laquicom02 (byron.cimav.edu.mx [148.223.46.1]) by yakko.cimav.edu.mx (Postfix) with SMTP id 1511476116 for >ccl.net>; Wed, 6 Aug 2003 14:48:25 -0600 (MDT) Message-ID: <011401c35c53$84a6a2e0$8400000a@laquicom02> From: "Dr. Daniel Glossman-Mitnik" >cimav.edu.mx> To: >ccl.net> Subject: program for superimposing molecules Date: Wed, 6 Aug 2003 14:46:51 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0111_01C35C29.928EC330" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 Disposition-Notification-To: "Dr. Daniel Glossman-Mitnik" >cimav.edu.mx> X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 This is a multi-part message in MIME format. ------=_NextPart_000_0111_01C35C29.928EC330 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear netters: I am looking for a Windows program for superimposing molecules. What I want to do is to make a comparison of two optimized Gaussian structures (small molecules=20 about 20-30 atoms) and get the RMS deviation. Any suggestion will be appreciated. Regards Dr. Daniel Glossman-Mitnik ********************************************************************** Dr. Daniel Glossman-Mitnik Centro de Investigaci=F3n en Materiales Avanzados (CIMAV) LAQUICOM - Laboratorio de Qu=EDmica Computacional Miguel de Cervantes 120 - Comp. Ind. 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_0111_01C35C29.928EC330 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear netters:
 
I am looking for a Windows program for=20 superimposing
molecules. What I want to do is to make = a=20 comparison
of  two optimized Gaussian = structures (small=20 molecules
about 20-30 atoms) and get the RMS=20 deviation.
 
Any suggestion will be = appreciated.
 
Regards
 
          &nbs= p;        =20 Dr. Daniel Glossman-Mitnik
 
 
****************************************************************= ******
Dr.=20 Daniel Glossman-Mitnik
Centro de Investigaci=F3n en Materiales = Avanzados=20 (CIMAV)
LAQUICOM - Laboratorio de Qu=EDmica Computacional
Miguel = de=20 Cervantes 120 - Comp. Ind. Chihuahua
Chihuahua, Chih. 31109 - = MEXICO
Tel.:=20 (52) 614 4391151
FAX: (52) 614 4391112
E-mail: >cimav.edu.mx">daniel.glossman<>cimav.edu.mx=
           = ;=20 >hotmail.com">glossman<>hotmail.com
 &n= bsp;         =20 >yahoo.com">dglossman<>yahoo.com
**********= ************************************************************
= ------=_NextPart_000_0111_01C35C29.928EC330--