From chemistry-request@server.ccl.net Thu Oct 10 11:50:09 2002 Received: from cornell.edu ([132.236.56.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9AFo9J21031 for ; Thu, 10 Oct 2002 11:50:09 -0400 Received: from cornell.edu (dopey.lassp.cornell.edu [128.84.241.121]) by cornell.edu (8.9.3/8.9.3) with ESMTP id LAA23701 for ; Thu, 10 Oct 2002 11:50:10 -0400 (EDT) Message-ID: <3DA5A1B1.15AF8305@cornell.edu> Date: Thu, 10 Oct 2002 11:50:09 -0400 From: Connie Chang X-Mailer: Mozilla 4.77 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Question about semi-empirical vs. tight-binding methods Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi -- I'm trying to find the vibrational modes of a molecule (~100 atoms) which has the elements carbon, nitrogen, oxygen, and cobalt in it. I've tried doing this through commercial programs such as Hyperchem and Gaussian, using the semi-empirical methods they provide (since the ab-initio methods are too computer-intensive); but I'm not getting sensible results. I suspect that part of the problem is because of the presence of the cobalt. My advisor wants me to write my own code now with the logic that code we write would be completely under our control as to what variables we tweak... My question is which method would be the best to do this. Are semi-empirical methods the same as tight-binding methods? I know that in tight binding methods, you use parameters for the Hamiltonian matrix elements. And that you need to find the specific parameters for the atom connectivity in your particular case. For example, since I have a carbon bonded to a nitrogen for my molecule, I need to find parameters specific to carbon-nitrogen connectivity. My question is is there a way in either the semi-empirical or tight binding methods where i would just need the parameters of the individual elements and there would be some systematic way for me to get the parameters *between* elements? Any suggestions, resources, etc. would be very helpful and appreciated. Thanks, Connie Chang cc236@cornell.edu From chemistry-request@server.ccl.net Thu Oct 10 00:20:27 2002 Received: from postoffice2.mail.cornell.edu ([132.236.56.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9A4KRJ00719 for ; Thu, 10 Oct 2002 00:20:27 -0400 Received: from cornell.edu (syr-24-58-45-234.twcny.rr.com [24.58.45.234]) by postoffice2.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id AAA28627 for ; Thu, 10 Oct 2002 00:20:25 -0400 (EDT) Sender: connie@cornell.edu Message-ID: <3DA5004A.85BD2D43@cornell.edu> Date: Thu, 10 Oct 2002 00:21:30 -0400 From: Connie Chang Reply-To: cc236@cornell.edu X-Mailer: Mozilla 4.78 [en] (X11; U; Linux 2.4.9-31 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Question about semi-empirical vs. tight-binding methods for a (100 atom) molecule Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi -- I am trying to find the vibrational modes of a 100 atom molecule that includes elements such as carbon, nitrogen, hydrogen, and cobalt (just one atom). I tried using commercial software such as Gaussian and Hyperchem, but was having trouble getting "sensible" answers with their semi-empirical methods and ab-initio methods proved to be too computer-intensive. I'm trying to write my own code to calculate energies (so that I can construct a hessian for the phonon spectra), but I'm not sure about the methods out there. Is tight-binding the same as the semi-empirical methods? I know that in tight binding, one needs to find the parameters for the elements in the molecule and the parameters for the particular atomic connectivity (so if my molecule has a carbon bonded to an oxygen, I would need the parameters for a carbon-oxygen connectivity). Is this how semi-empirical methods work as well? Or is there just a set of parameters for each element without taking into account the connectivity? Or is there some systematic way to derive parameters between elements? Any advice about what method to use or resources that I can look at would be much appreciated. -Connie Chang From chemistry-request@server.ccl.net Thu Oct 10 09:58:06 2002 Received: from natcn1.bscexc1.bsci.com ([204.155.16.114]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9ADw6J17482 for ; Thu, 10 Oct 2002 09:58:06 -0400 Received: by natcn1.bscexc1.bsci.com with Internet Mail Service (5.5.2653.19) id <43T97CMD>; Thu, 10 Oct 2002 09:58:02 -0400 Message-ID: <08B0F738C9848346965E4B75D0699615037E9D08@natpr6> From: "Song, Young-Ho" To: "'chemistry@ccl.net'" Subject: Rapamycin LogP Date: Thu, 10 Oct 2002 09:59:00 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C27065.2F395710" 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_01C27065.2F395710 Content-Type: text/plain; charset="iso-8859-1" Hi; I was trying to find out the LogP of Rapamycin (CAS 53123-88-9 ) but without any success. I need this quite urgently. Can you help me with this? Thanks very much for your help in advance. Young ------_=_NextPart_001_01C27065.2F395710 Content-Type: text/html; charset="iso-8859-1"
Hi;
I was trying to find out the LogP of Rapamycin (CAS 53123-88-9
) but without any success. I need this quite urgently.
 
Can you help me with this?
 
Thanks very much for your help in advance.
 
Young
 
------_=_NextPart_001_01C27065.2F395710-- From chemistry-request@server.ccl.net Thu Oct 10 06:41:55 2002 Received: from mail.jadeinc.com ([209.57.24.15]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9AAfsJ12105 for ; Thu, 10 Oct 2002 06:41:55 -0400 Received: from igor.jadeinc.com [209.57.24.236] by mail.jadeinc.com with ESMTP (SMTPD32-6.06) id A8EF507E006A; Thu, 10 Oct 2002 06:39:43 -0400 Message-Id: <5.1.1.2.2.20021010063915.00a00ec0@mail.jadeinc.com> X-Sender: smolnar@mail.jadeinc.com X-Mailer: QUALCOMM Windows Eudora Version 5.1.1.3 (Beta) Date: Thu, 10 Oct 2002 06:40:48 -0400 To: Chemistry@ccl.net From: "Stephen P. Molnar, Ph.D." Subject: GAMESS on a Laptop Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed I've posted this note to the GAMESS list with no results, so I thought that I'd try the CCL list. I've been using GAMESS for some years now, but not on a laptop until now. I compiled the most recent version to run in a Linux SuSE v8.0 environment. The compilation process went smoothly without any apparent hitches, but when I attempted a test I got: ----- GAMESS execution script ----- This job is running on host inga at Thu Sep 26 00:52:35 EDT 2002 Available scratch disk space (Kbyte units) at beginning of the job is Filesystem 1k-blocks Used Available Use% Mounted on /dev/hda3 10606352 1691328 8915024 16% / cp exam01.inp /usr/src/Gamess/gamess/scr/exam01.F05 unset echo setenv EXTBAS /dev/null setenv IRCDATA ~/scr/exam01.irc setenv INPUT /usr/src/Gamess/gamess/scr/exam01.F05 setenv PUNCH ~/scr/exam01.dat setenv AOINTS /usr/src/Gamess/gamess/scr/exam01.F08 setenv MOINTS /usr/src/Gamess/gamess/scr/exam01.F09 setenv DICTNRY /usr/src/Gamess/gamess/scr/exam01.F10 setenv DRTFILE /usr/src/Gamess/gamess/scr/exam01.F11 setenv CIVECTR /usr/src/Gamess/gamess/scr/exam01.F12 setenv CASINTS /usr/src/Gamess/gamess/scr/exam01.F13 setenv CIINTS /usr/src/Gamess/gamess/scr/exam01.F14 setenv WORK15 /usr/src/Gamess/gamess/scr/exam01.F15 setenv WORK16 /usr/src/Gamess/gamess/scr/exam01.F16 setenv CSFSAVE /usr/src/Gamess/gamess/scr/exam01.F17 setenv FOCKDER /usr/src/Gamess/gamess/scr/exam01.F18 setenv DASORT /usr/src/Gamess/gamess/scr/exam01.F20 setenv DFTINTS /usr/src/Gamess/gamess/scr/exam01.F21 setenv DFTGRID /usr/src/Gamess/gamess/scr/exam01.F22 setenv JKFILE /usr/src/Gamess/gamess/scr/exam01.F23 setenv ORDINT /usr/src/Gamess/gamess/scr/exam01.F24 setenv EFPIND /usr/src/Gamess/gamess/scr/exam01.F25 setenv PCMDATA /usr/src/Gamess/gamess/scr/exam01.F26 setenv PCMINTS /usr/src/Gamess/gamess/scr/exam01.F27 setenv MLTPL /usr/src/Gamess/gamess/scr/exam01.F28 setenv MLTPLT /usr/src/Gamess/gamess/scr/exam01.F29 setenv DAFL30 /usr/src/Gamess/gamess/scr/exam01.F30 setenv SOINTX /usr/src/Gamess/gamess/scr/exam01.F31 setenv SOINTY /usr/src/Gamess/gamess/scr/exam01.F32 setenv SOINTZ /usr/src/Gamess/gamess/scr/exam01.F33 setenv SORESC /usr/src/Gamess/gamess/scr/exam01.F34 setenv SIMEN ~/scr/exam01.simen setenv SIMCOR ~/scr/exam01.simcor setenv GCILIST /usr/src/Gamess/gamess/scr/exam01.F37 setenv SOCCDAT /usr/src/Gamess/gamess/scr/exam01.F40 setenv AABB41 /usr/src/Gamess/gamess/scr/exam01.F41 setenv BBAA42 /usr/src/Gamess/gamess/scr/exam01.F42 setenv BBBB43 /usr/src/Gamess/gamess/scr/exam01.F43 setenv MCQD50 /usr/src/Gamess/gamess/scr/exam01.F50 setenv MCQD51 /usr/src/Gamess/gamess/scr/exam01.F51 setenv MCQD52 /usr/src/Gamess/gamess/scr/exam01.F52 setenv MCQD53 /usr/src/Gamess/gamess/scr/exam01.F53 setenv MCQD54 /usr/src/Gamess/gamess/scr/exam01.F54 setenv MCQD55 /usr/src/Gamess/gamess/scr/exam01.F55 setenv MCQD56 /usr/src/Gamess/gamess/scr/exam01.F56 setenv MCQD57 /usr/src/Gamess/gamess/scr/exam01.F57 setenv MCQD58 /usr/src/Gamess/gamess/scr/exam01.F58 setenv MCQD59 /usr/src/Gamess/gamess/scr/exam01.F59 setenv MCQD60 /usr/src/Gamess/gamess/scr/exam01.F60 setenv MCQD61 /usr/src/Gamess/gamess/scr/exam01.F61 setenv MCQD62 /usr/src/Gamess/gamess/scr/exam01.F62 setenv MCQD63 /usr/src/Gamess/gamess/scr/exam01.F63 setenv MCQD64 /usr/src/Gamess/gamess/scr/exam01.F64 setenv CCREST /usr/src/Gamess/gamess/scr/exam01.F70 setenv CCDIIS /usr/src/Gamess/gamess/scr/exam01.F71 setenv CCINTS /usr/src/Gamess/gamess/scr/exam01.F72 setenv CCT1AMP /usr/src/Gamess/gamess/scr/exam01.F73 setenv CCT2AMP /usr/src/Gamess/gamess/scr/exam01.F74 setenv CCT3AMP /usr/src/Gamess/gamess/scr/exam01.F75 setenv CCVM /usr/src/Gamess/gamess/scr/exam01.F76 setenv CCVE /usr/src/Gamess/gamess/scr/exam01.F77 unset echo ddikick.x exam01 /usr/src/Gamess/gamess gamess.01.x /usr/src/Gamess/gamess/scr/ 1 inga Initiating 1 compute processes to run job exam01 Executable gamess.01.x will be run from directory /usr/src/Gamess/gamess Working scratch directory on each host will be /usr/src/Gamess/gamess/scr/ Running gamess.01.x on inga as compute process 0 Connect to kickoff socket by process 0 has failed, error 101 ddikick: Trapped SIGCHLD: Unexpected termination of a child process. What is an error 101? How is it corrected? Thanks in advance From chemistry-request@server.ccl.net Thu Oct 10 14:10:40 2002 Received: from cornell.edu ([132.236.56.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9AIAeJ25185 for ; Thu, 10 Oct 2002 14:10:40 -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 OAA06020; Thu, 10 Oct 2002 14:10:03 -0400 (EDT) Sender: cc236@cornell.edu Message-ID: <3DA5C27A.311EAAA2@cornell.edu> Date: Thu, 10 Oct 2002 14:10:02 -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: Thomas.Heine@chemie.tu-dresden.de, chemistry@ccl.net Subject: Re: CCL:Question about semi-empirical vs. tight-binding methods References: <3DA5A1B1.15AF8305@cornell.edu> <3DA5C139.2080900@chemie.tu-dresden.de> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Thomas -- Thanks for the reply. I'm still really learning about all of this... Do you know if tight-binding (which physicists use) and semi-empirical methods like PM3, CNDO, etc. (which chemists use) are in fact the same? Also, is it sufficient to get parameters for the individual elements in the molecule or are parameters describing an element's connection to another element needed? Again, thanks. Connie Thomas Heine wrote: > Hi, > > I can provide a code and CHN parameters, but Co is not parameterised afaik. > > You might ask Marcus Elstner (m.elstner@dkfz-heidelberg.de), he is > working on biological systems using a TB method. > > Good luck > Thomas > > Connie Chang schrieb: > > Hi -- > > > > I'm trying to find the vibrational modes of a molecule (~100 atoms) > > which has the elements carbon, nitrogen, oxygen, and cobalt in it. I've > > tried doing this through commercial programs such as Hyperchem and > > Gaussian, using the semi-empirical methods they provide (since the > > ab-initio methods are too computer-intensive); but I'm not getting > > sensible results. I suspect that part of the problem is because of the > > presence of the cobalt. > > > > My advisor wants me to write my own code now with the logic that code we > > write would be completely under our control as to what variables we > > tweak... My question is which method would be the best to do this. > > > > Are semi-empirical methods the same as tight-binding methods? I know > > that in tight binding methods, you use parameters for the Hamiltonian > > matrix elements. And that you need to find the specific parameters for > > the atom connectivity in your particular case. For example, since I > > have a carbon bonded to a nitrogen for my molecule, I need to find > > parameters specific to carbon-nitrogen connectivity. My question is is > > there a way in either the semi-empirical or tight binding methods where > > i would just need the parameters of the individual elements and there > > would be some systematic way for me to get the parameters *between* > > elements? > > > > Any suggestions, resources, etc. would be very helpful and appreciated. > > > > Thanks, > > Connie Chang > > cc236@cornell.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 Thu Oct 10 16:35:48 2002 Received: from chem.udel.edu ([128.175.138.224]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9AKZmJ28367 for ; Thu, 10 Oct 2002 16:35:48 -0400 Received: from localhost (pradyu@localhost) by chem.udel.edu (8.9.3/8.9.3) with ESMTP id QAA166406 for ; Thu, 10 Oct 2002 16:56:10 -0400 (EDT) Date: Thu, 10 Oct 2002 16:56:10 -0400 From: "Pradyumna S. Singh" To: Chemistry@ccl.net Subject: SCIPCM Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I have been trying (unsuccessfully !) to do some ab initio studies on trans-2,3-dinitro butene in solution. Typically I've employed DFT level of theory with 6-31G basis set, and the SCIPCM model; Gaussian98.A11 However it has been impossible to optimise the structure in solution (using the SCIPCM). What I usually end up with is the following : ----------------------------------------------------------------------------- E=-0.111166749562117D+04 DIIS: error= 3.26D-01 at cycle 1. Fock symm off for IB=2 I1= 3 I= 113 J= 83 Cut=1.00D-04 Err=2.02D-04 Fock matrix is not symmetric: symmetry in diagonalization turned off. T= 2927. Gap= 0.012 NK=0 IS= 1 IE= 220 NO(<0.9)= 1 NV(>0.1)= 1 38.63e < EF 0.37e >EF Err=5.6D-11 RMSDP=2.01D+00 MaxDP=1.14D+02 Density matrix breaks symmetry, PCut= 1.00D-04 Density matrix has no symmetry -- integrals replicated. Cycle 2 Pass 1 IDiag 1: RMSU= 1.92D+00 CP: 3.00D+00 Compute SCI-PCM surface. WARNING! Serious error in surface integrals. It is probable that some of the solute is outside the cavity and/or parts of the cavity surface cannot be reached from the origin. Try more integration points or a different set of integration origins. Surface Problems in SciFoc ------------------------------------------------------------------------------- Could someone kindly point out what the problem here is, and what could be changed to make it work ? Any help/leads in the matter would be much appreciated. Thanks, Pradyumna