From chemistry-request@server.ccl.net Wed Nov 14 05:42:46 2001 Received: from ns2.tudelft.nl ([130.161.180.65]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAEAgjB17697 for ; Wed, 14 Nov 2001 05:42:46 -0500 Received: from listserv.tudelft.nl (listserv.tudelft.nl [130.161.180.33]) by mailhost1.tudelft.nl (PMDF V6.0-025 #37171) with ESMTP id <0GMS009EDDR3SS@mailhost1.tudelft.nl> for chemistry@ccl.net; Wed, 14 Nov 2001 11:42:39 +0100 (MET) Received: from stm-ltc2.dct.tudelft.nl (stm-ltc2.dct.tudelft.nl [130.161.196.198]) by listserv.tudelft.nl (8.10.2+Sun/8.10.2) with ESMTP id fAEAgcj05103 for ; Wed, 14 Nov 2001 11:42:39 +0100 (MET) Received: from STM-LTC2/SpoolDir by stm-ltc2.dct.tudelft.nl (Mercury 1.47) ; Wed, 14 Nov 2001 11:42:39 +0000 (MET-1MEST) Received: from SpoolDir by STM-LTC2 (Mercury 1.47); Wed, 14 Nov 2001 11:42:37 +0000 (MET-1MEST) Date: Wed, 14 Nov 2001 11:42:32 +0100 From: Martijn Zwijnenburg Subject: solvent models in G98, comparison To: chemistry@ccl.net Message-id: <3BF258A8.7617.5FCDAB@localhost> MIME-version: 1.0 X-Mailer: Pegasus Mail for Win32 (v3.12c) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Priority: normal Dear all, I'm very interested in calculating solution properties of molecules by means of SCRF in Gaussian 98. However, there are various models and I'm not sure of there merits. I've looked through the literature but have been unable to find a review article comparing the different methods. Does somebody know where to find such an article?? Gr. Martijn ------------------------------------------------------------------------- Martijn Zwijnenburg Lab. of Applied Organic Chemistry and Catalysis Delft University of Technology Julianalaan 136 2628 BL Delft The Netherlands Tel: 0031-(0)152782691 Fax: 0031-(0)152784700 e-mail: M.A.Zwijnenburg@tnw.tudelft.nl web page: http://come.to/tock From chemistry-request@server.ccl.net Wed Nov 14 07:16:53 2001 Received: from MAIL.AD.Berry.edu ([66.20.28.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAECGrB19542 for ; Wed, 14 Nov 2001 07:16:53 -0500 Received: from [10.16.232.24] ([10.16.232.24]) by MAIL.AD.Berry.edu with Microsoft SMTPSVC(5.0.2195.2966); Wed, 14 Nov 2001 07:17:28 -0500 User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 Date: Wed, 14 Nov 2001 07:16:46 -0500 Subject: Bonds vs No Bonds in Minimized Structures From: Gary Breton To: Message-ID: Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit X-OriginalArrivalTime: 14 Nov 2001 12:17:28.0745 (UTC) FILETIME=[53DF2990:01C16D06] Hello all, I have been conducting some geometry minimizations on some 1,2-diazacyclobutane structures using Gaussian98 with the GaussView GUI. When I minimize the parent compound (1,2-diazacyclobutane with N-H bonds) at the RHF631G* level, everything looks fine. If, however, I minimize at the RB3LYP6311+G** level, a similar structure to the HF minimization results, but GaussView does NOT SHOW a bond between the two nitrogen atoms. The bond has apparently not broken since the molecule adopts a geometry as if its still there (i.e., in the HF minimization the N-N, C-N and C-C bond lengths are 1.45405, 1.47272 and 1.53174, respectively, while in the B3LYP they are 1.49052, 1.49351 and 1.53844, respectively). Furthermore, if I start with the HF structure and further minimize at the B3LYP level, the bond again disappears! If I start with the B3LYP structure and ADD a N-N bond and then re-minimize, it again eliminates the bond. Is there any significance to the presence or absence of the bond? Why would GaussView not put a bond into the structure? Thanks and best regards! Gary W. Breton Chair and Associate Professor Department of Chemistry Berry College PO Box 495016 Mount Berry, GA 30149 "There's a light at the end of the tunnel, but it may be an oncoming train" From chemistry-request@server.ccl.net Wed Nov 14 07:30:22 2001 Received: from xena.oai.co.uk ([195.172.92.249]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAECUIB19903 for ; Wed, 14 Nov 2001 07:30:22 -0500 Received: by XENA with Internet Mail Service (5.5.2650.21) id ; Wed, 14 Nov 2001 12:29:52 -0000 Message-ID: <5FD8C12EECBBD4119DD10002B3027B9A667E41@GABRIELLE> From: "Robinson, James" To: "'Gary Breton'" , CHEMISTRY@ccl.net Subject: RE: Bonds vs No Bonds in Minimized Structures Date: Wed, 14 Nov 2001 12:29:48 -0000 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Guassview merely add lines between two points in space. The question of whether a bond is really there is not one to be addressed with the viewing program. Perhaps bader bond-critical-point analysis may help answer the bonding question. Does MP2 affect things? Keep an open mind, don't be fooled by the pretty pictures alone. J -----Original Message----- From: Gary Breton [mailto:gbreton@berry.edu] Sent: Wednesday, November 14, 2001 12:17 PM To: CHEMISTRY@ccl.net Subject: CCL:Bonds vs No Bonds in Minimized Structures Hello all, I have been conducting some geometry minimizations on some 1,2-diazacyclobutane structures using Gaussian98 with the GaussView GUI. When I minimize the parent compound (1,2-diazacyclobutane with N-H bonds) at the RHF631G* level, everything looks fine. If, however, I minimize at the RB3LYP6311+G** level, a similar structure to the HF minimization results, but GaussView does NOT SHOW a bond between the two nitrogen atoms. The bond has apparently not broken since the molecule adopts a geometry as if its still there (i.e., in the HF minimization the N-N, C-N and C-C bond lengths are 1.45405, 1.47272 and 1.53174, respectively, while in the B3LYP they are 1.49052, 1.49351 and 1.53844, respectively). Furthermore, if I start with the HF structure and further minimize at the B3LYP level, the bond again disappears! If I start with the B3LYP structure and ADD a N-N bond and then re-minimize, it again eliminates the bond. Is there any significance to the presence or absence of the bond? Why would GaussView not put a bond into the structure? Thanks and best regards! Gary W. Breton Chair and Associate Professor Department of Chemistry Berry College PO Box 495016 Mount Berry, GA 30149 "There's a light at the end of the tunnel, but it may be an oncoming train" -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Wed Nov 14 03:51:28 2001 Received: from vytautas.vdu.lt ([193.219.38.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAE8pQB14629 for ; Wed, 14 Nov 2001 03:51:26 -0500 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp id 163vlD-0005uW-00; Wed, 14 Nov 2001 10:51:07 +0200 Received: from vejas (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id LAA26368; Wed, 14 Nov 2001 11:33:29 +0200 (GMT) Date: Wed, 14 Nov 2001 10:51:03 +0200 From: a3arzi X-Mailer: The Bat! (v1.44) UNREG / CD5BF9353B3B7091 Reply-To: "Art'" X-Priority: 3 (Normal) Message-ID: <105727035.20011114105103@vaidila.vdu.lt> To: CCL CC: Arthur Olson Subject: CCL: AutoDock 3.x results interpretation Mime-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 X-MIME-Autoconverted: from 8bit to quoted-printable by vaidila.vdu.lt id LAA26368 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id fAE8pSB14630 Dear all, Some dimness arised about the final docking results. After AutoDock (AD) run, log file contains histogram: 1. Does it mean that the lowest energy (the 1st cluster) is the global minimum of protein for that ligand ??? 2. How interpret the clusters (with higher energy, i.e. less favorable conformations) with larger number of individuals after many runs of GA ????? Maybe, the best determinated site for the ligand in protein is the derivation of lowest docked energy (LDE) and number of individuals in cluster ???? I have 5000000 evaluations, 35000 generations and made 300 runs (grid spacing 0.6Å), but the 'best site' - i.e. with lowest LDE - contains only 2 structures...... I thought increasing the number of mentioned parameters, all structures should tend to accumulate at the the clusters with lowest energy ..... ??? Could anyone share some thoughts ? CLUSTERING HISTOGRAM ____________________ ________________________________________________________________________________ | | | | | Clus | Lowest | Run | Mean | Num | Histogram -ter | Docked | | Docked | in | Rank | Energy | | Energy | Clus| 5 10 15 20 25 30 35 _____|___________|_____|___________|_____|____:____|____:____|____:____|____:___ 1 | -7.86 | 148 | -7.83 | 2 |## 2 | -7.62 | 278 | -7.55 | 12 |############ 3 | -7.55 | 227 | -7.32 | 24 |######################## 4 | -7.52 | 207 | -7.51 | 3 |### 5 | -7.26 | 115 | -7.23 | 23 |####################### 6 | -7.22 | 88 | -7.15 | 9 |######### 7 | -7.17 | 47 | -7.05 | 6 |###### 8 | -7.15 | 70 | -7.15 | 1 |# 9 | -7.14 | 168 | -7.14 | 1 |# Thank you all and best regards Arturas Z. From chemistry-request@server.ccl.net Wed Nov 14 04:23:05 2001 Received: from uscmail.usc.es ([193.144.75.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAE9N4B15922 for ; Wed, 14 Nov 2001 04:23:04 -0500 Received: from desoft1 (desoft01.usc.es [193.144.82.147]) by uscmail.usc.es (8.9.1/8.9.1) with SMTP id KAA23651 for ; Wed, 14 Nov 2001 10:22:54 +0100 (MET) Message-ID: <003401c16cee$a2f00620$935290c1@usc.es> From: "Armando Navarro" To: "ccl" Subject: Summary for complex exp(x2)dx integrals Date: Wed, 14 Nov 2001 10:27:49 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0031_01C16CF7.0269BAD0" 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 This is a multi-part message in MIME format. ------=_NextPart_000_0031_01C16CF7.0269BAD0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear members: Here the summary for the question on complex exp(x2)dx. Thanks to all = people The original question: Dear Members: Can anybody point me to routines (or simply numerical algorithms) for = solution of complex integrals of the form: int (exp(x2)dx) , with limits between 0 and z, being z a complex number = of the form a+bi.=20 The text in the paper says that this integral can be related to complex = error function, however I was not capable to establish the relationship. Thanks in advance Armando Navarro Facultade de Quimica Departamento de quimica Organica Universidade de Santiago de Compostela. Spain e-mail: qoajnv@usc.es ---------------------------------------------- > From Robert Waterland: Armando: Equation 7.1.3 in Handbook of Mathematical Functions by Abramowitz and Stegun is w(z) =3D exp(-z^2) (1+ 2i/sqrt(pi)*INT) =3D exp(-z^2)erfc(-iz) where INT is the integral you are looking for, i.e. int(exp(x^2)dx) between 0 and z. So the integral you want is related to the Complementary Error function with complex argument. Abramowitz and Stegun have a number of series forms for the Error = function which (I believe) can be used for complex arguments. See section 7.5 examples 12 to 19 for use of tables and series for complex arguments. There is also a table (Table 7.9) of w(z) for complex arguments = (z=3Dx+iy) where 0<=3Dx<=3D1 and 0<=3Dy<=3D3) so you can test the series formulae = to see if they work. Rob -------------------------------------------------------------- > From Gerd Raether: Please look in the "bible" - numerical recipes - you can download pages in ps/pdf format from http://www.nr.com/ For complex integration you might need also the residue theorem - see a textbook for complex analysis. Hope this helps somewhat, Gerd ----------------------------------------------------------- > From Bruno Sopko: Try GPL Bruno Sopko ------------------------------------------------------------ > From Tom Sundius: The complex error function of Faddeyeva and Terent'ev is defined as w(z)=3Dexp(-z^2)(1+(2i/sqrt(pi))*int_0^z (exp(t^2)dt)). It is also = expressed as exp(-z^2)*erfc(-iz), where erfc is the complementary error function (erfc z =3D 1 - erf z). There is a chapter about the error function in the Handbook of Mathematical Tables by Abramowitz and Stegun. This = chapter was written by Walter Gautschi, who also wrote an efficient algorithm to compute it to ten decimals (see SIAM J. Numer. Analysis 7, 187-198 = (1970)). An even more efficient algorithm has been published by Poppe and Wijers (Fortran version in http://www.netlib.org/toms/680) The real part of the complex error function is related to the Voigt function (see, for instance, T. Sundius: J.Raman Spectrosc. 1, 471-488 = (1973)). Greetings, TS Tom Sundius University of Helsinki, Dept of Physical Sciences phone +358-9-191 = 50672 P.O.Box 64, FIN-00014 Helsinki, Finland fax +358-9-191 = 50610 ------=_NextPart_000_0031_01C16CF7.0269BAD0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear members:
Here the summary for the question on = complex=20 exp(x2)dx. Thanks to all people
 
The original question:
Dear Members:
Can anybody point me to routines (or = simply=20 numerical algorithms) for solution of complex integrals of the=20 form:
 
int (exp(x2)dx) , with limits between 0 = and z,=20 being z a complex number of the form a+bi.
The text in the paper says that this = integral can=20 be related to complex error function, however I was not capable to = establish the=20 relationship.
 
Thanks in advance
Armando Navarro
Facultade de Quimica
Departamento de quimica = Organica
Universidade de Santiago de Compostela. = Spain
e-mail: qoajnv@usc.es
 
----------------------------------------------
From Robert Waterland:
Armando:

Equation 7.1.3 in  Handbook of Mathematical = Functions=20 by Abramowitz and
Stegun is

w(z) =3D exp(-z^2) (1+ = 2i/sqrt(pi)*INT) =3D=20 exp(-z^2)erfc(-iz)

where INT is the integral you are looking = for, =20 i.e. int(exp(x^2)dx)
between 0 and z.

So the integral you want = is=20 related to the Complementary Error function
with complex=20 argument.

Abramowitz and Stegun have a number of series forms for = the=20 Error function
which (I believe) can be used for complex = arguments.  See=20 section 7.5
examples 12 to 19 for use of tables and series for = complex=20 arguments.
There is also a table (Table 7.9) of w(z) for complex = arguments=20 (z=3Dx+iy)
where 0<=3Dx<=3D1 and 0<=3Dy<=3D3) so you can = test the series=20 formulae to see if
they work.

Rob
--------------------------------------------------------------
From Gerd Raether:
Please look in the "bible" - numerical recipes - you can download=20 pages
in ps/pdf format from

http://www.nr.com/

For complex = integration=20 you might need also the
residue theorem - see a textbook for complex=20 analysis.

Hope this helps somewhat,

Gerd
-----------------------------------------------------------
From Bruno Sopko:
 
Try GPL
Bruno Sopko
------------------------------------------------------------
From Tom Sundius:
 
The complex error function of Faddeyeva and Terent'ev is defined=20 as
w(z)=3Dexp(-z^2)(1+(2i/sqrt(pi))*int_0^z (exp(t^2)dt)). It is also = expressed
as exp(-z^2)*erfc(-iz), where erfc is the complementary = error=20 function
(erfc z =3D 1 - erf z). There is a chapter about the error = function=20 in
the Handbook of Mathematical Tables by Abramowitz and Stegun. This = chapter
was written by Walter Gautschi, who also wrote an efficient = algorithm=20 to
compute it to ten decimals (see SIAM J. Numer. Analysis 7, 187-198 = (1970)).
An even more efficient algorithm has been published by Poppe = and=20 Wijers
(Fortran version in http://www.netlib.org/toms/680)

The=20 real part of the complex error function is related to the = Voigt
function=20 (see, for instance, T. Sundius: J.Raman Spectrosc. 1, 471-488=20 (1973)).


   =20 Greetings,

      TS

Tom=20 Sundius
University of Helsinki, Dept of Physical Sciences   = phone=20 +358-9-191 50672
P.O.Box 64, FIN-00014 Helsinki,=20 Finland           =  =20 fax   +358-9-191 50610

------=_NextPart_000_0031_01C16CF7.0269BAD0-- From chemistry-request@server.ccl.net Wed Nov 14 08:47:09 2001 Received: from hpserv.imim.es ([193.144.6.104]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAEDl8B21754 for ; Wed, 14 Nov 2001 08:47:08 -0500 Received: from imim.es (i21.imim.es [193.147.240.127]) by hpserv.imim.es with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id V0GD1B9R; Wed, 14 Nov 2001 14:47:52 +0100 Sender: hteran@ccl.net Message-ID: <3BF274F5.459F8@imim.es> Date: Wed, 14 Nov 2001 14:43:17 +0100 From: "Hugo G. de Teran" X-Mailer: Mozilla 4.72 [en] (X11; U; Linux 2.2.14-5.0 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Autodock errors: the answer Content-Type: multipart/alternative; boundary="------------541E97F17718CA076F2534FE" --------------541E97F17718CA076F2534FE Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear all, I sumarize the answers to my question, perhaps it may help autodock users that find the same problem: QUESTION: > When running autodock, I found the next problem: > > DPF> ga_run 10 # do this many GA or LGA runs > > NOTE: Command mode has been set. Sorry, genetic algorithm-local search cannot be performed. > > DPF> > DPF> # Perform Cluster Analysis > > > DPF> analysis # do cluster analysis on results > > NOTE: Command mode has been set, so cluster analysis cannot be performed. > > >>> Closing the docking parameter file (DPF)... > > ________________________________________________________________________________ > > /usr/local/modelling/AutoDock_3.0/bin/sgi4D.IRIX64_6.5_R10000/autodock3: NOW IN COMMAND MODE. > > And The calculation stays on standby. > ANSWERS: > From Frank Beierlein > Hi Hugo, > possibly the filename of your *.dpf file has too many characters. Shortening the filename might help. > Best regards, > Frank > Thanks a lot, such a simple thing was the problem!!! From "Garrett M. Morris" > You must have used the '-c' flag when you executed autodock3 from the > UNIX command line, otherwise AutoDock could not go into command mode. > > This is not an error: AutoDock is waiting for you to give it a > command: e.g. you could type "epdb aspirin.pdbq" and AutoDock would > compute the energy of interaction between the molecule in the PDBQ > file you specified and the receptor represented by the grid maps > specified in your DPF. Type "quit" and AutoDock will terminate > normally. > > This was not the case, but it is usefull to now about this flag, thanks. > From Christian.Pilger@bc.boehringer-ingelheim.com > Dear Hugo, > > did you use the pre-compiled executable of autodock that comes with the > distribution or did you re-compile the source code ? I remember having faced > a similiar problem with the command mode of autodock when I employed a > re-compiled executable on an XP1000 Alpha machine. Unfortunately, we were > unable to solve that problem. But the pre-compiled versions in the > distribution worked nicely for us. > > Regards, > > Christian > I had used the re-compiled version, I did not find any pre-compiled one. Thanks all for your answers, Hope this helps anyone Hugo -- Hugo G. de Teran Castañon G. R. Informatica Biomedica Institut Municipal d'Investigacio Medica - IMIM C/ Dr Aiguader, 80, E-08003/ Barcelona (SPAIN) Ph: +34 93 221 10 09 ext 2340 Fax: +34 93 221 3237 http://www1.imim.es/modeling/ --------------541E97F17718CA076F2534FE Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all,
I sumarize the answers to my question, perhaps it may help autodock users that find the same problem:

QUESTION:
  

  When running autodock, I found the next problem: 

  DPF> ga_run 10          # do this many GA or LGA runs 

  NOTE: Command mode has been set.  Sorry, genetic algorithm-local search cannot be performed. 

  DPF> 
  DPF> # Perform Cluster Analysis 
    

  DPF> analysis           # do cluster analysis on results 

  NOTE: Command mode has been set, so cluster analysis cannot be performed. 

  >>> Closing the docking parameter file (DPF)... 

  ________________________________________________________________________________ 

  /usr/local/modelling/AutoDock_3.0/bin/sgi4D.IRIX64_6.5_R10000/autodock3: NOW IN COMMAND MODE. 

  And The calculation stays on standby.


ANSWERS:

From  Frank Beierlein <Frank.Beierlein@organik.uni-erlangen.de> 

Hi Hugo,
possibly the filename of your *.dpf file has too many characters. Shortening the filename might help. 
Best regards,
Frank


Thanks a lot, such a simple thing was the problem!!!
 

 From  "Garrett M. Morris" <garrett@scripps.edu> 

You must have used the '-c' flag when you executed autodock3 from the
UNIX command line, otherwise AutoDock could not go into command mode.

This is not an error: AutoDock is waiting for you to give it a
command: e.g. you could type "epdb aspirin.pdbq" and AutoDock would
compute the energy of interaction between the molecule in the PDBQ
file you specified and the receptor represented by the grid maps
specified in your DPF.  Type "quit" and AutoDock will terminate
normally.


This was not the case, but it is usefull to now about this flag, thanks.

From Christian.Pilger@bc.boehringer-ingelheim.com
  

Dear Hugo,

did you use the pre-compiled executable of autodock that comes with the
distribution or did you re-compile the source code ? I remember having faced
a similiar problem with the command mode of autodock when I employed a
re-compiled executable on an XP1000 Alpha machine. Unfortunately, we were
unable to solve that problem. But the pre-compiled versions in the
distribution worked nicely for us.

Regards,

Christian
I had used the re-compiled version, I did not find any pre-compiled one.
Thanks all for your answers,
Hope this helps anyone

Hugo

--  Hugo G. de Teran Castañon
G. R. Informatica Biomedica Institut Municipal d'Investigacio Medica - IMIM C/ Dr Aiguader, 80, E-08003/ Barcelona (SPAIN)
Ph: +34 93 221 10 09 ext 2340
Fax: +34 93 221 3237                                          http://www1.imim.es/modeling/ --------------541E97F17718CA076F2534FE-- From chemistry-request@server.ccl.net Wed Nov 14 09:29:15 2001 Received: from pollux.chem.umn.edu ([128.101.156.56]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAEETFB22901 for ; Wed, 14 Nov 2001 09:29:15 -0500 Received: (from cramer@localhost) by pollux.chem.umn.edu (8.9.3/8.9.3) id IAA18760; Wed, 14 Nov 2001 08:29:07 -0600 (CST) From: Christopher Cramer Message-Id: <200111141429.IAA18760@pollux.chem.umn.edu> Subject: Re: CCL:solvent models in G98, comparison To: M.A.Zwijnenburg@tnw.tudelft.nl (Martijn Zwijnenburg) Date: Wed, 14 Nov 2001 08:29:07 -0600 (CST) Cc: chemistry@ccl.net In-Reply-To: <3BF258A8.7617.5FCDAB@localhost> from "Martijn Zwijnenburg" at Nov 14, 2001 11:42:32 AM X-Mailer: ELM [version 2.5 PL2] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Martijn, > > I'm very interested in calculating solution properties of molecules > by means of SCRF in Gaussian 98. However, there are various > models and I'm not sure of there merits. I've looked through the > literature but have been unable to find a review article comparing > the different methods. Does somebody know where to find such an > article?? > You may find our review Cramer, C. J.; Truhlar, D. G. "Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics" Chem. Rev. 1999, 99, 2160. helpful in this regard. And, for those interested in solvation models NOT in G98 (and also one that in theory IS to be implemented in Gxx at some future point), comp.chem.umn.edu/solvation may prove of interest. Best regards, Chris -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-2006 cramer@pollux.chem.umn.edu http://pollux.chem.umn.edu/~cramer (website includes information about new textbook "Essentials of Computational Chemistry: Theories and Models") From chemistry-request@server.ccl.net Wed Nov 14 10:46:02 2001 Received: from hschipaa.hsc.usf.edu ([131.247.16.97]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fAEFk1B24877 for ; Wed, 14 Nov 2001 10:46:01 -0500 Received: from hschipaa.hsc.usf.edu ([131.247.16.105]) by hsc.usf.edu (8.9.3+Sun/8.9.3) with SMTP id KAA28732 for ; Wed, 14 Nov 2001 10:45:54 -0500 (EST) Message-ID: <3BF291B2.6DA7C211@mindless.com> Date: Wed, 14 Nov 2001 10:45:54 -0500 From: David Smith X-Mailer: Mozilla 4.78 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: creating pdbs Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello all, Does anyone know of a free program (linux/windows) which can create (or edit) small molecule pdb files. I've looked at many programs but have found none. Thanks for all suggestions. David Smith From chemistry-request@server.ccl.net Wed Nov 14 11:19:01 2001 Received: from Salicet.ucd.ie ([137.43.1.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAEGJ1B25643 for ; Wed, 14 Nov 2001 11:19:01 -0500 X-Confirm-reading-to: Laurence.Cuffe@ucd.ie X-PMrqc: 1 Received: from CONVERSION-DAEMON.Salicet.ucd.ie by Salicet.ucd.ie (PMDF V6.0-24 #36961) id <0GMS00401OAHK1@Salicet.ucd.ie> for CHEMISTRY@ccl.net; Wed, 14 Nov 2001 14:30:26 +0000 (GMT) Received: from elvira.ucd.ie ([137.43.24.26]) by Salicet.ucd.ie (PMDF V6.0-24 #36961) with ESMTP id <0GMS00KIOOAG8D@Salicet.ucd.ie>; Wed, 14 Nov 2001 14:30:16 +0000 (GMT) Date: Wed, 14 Nov 2001 14:31:03 +0000 From: Laurence Cuffe Subject: Re: CCL:Bonds vs No Bonds in Minimized Structures In-reply-to: To: Gary Breton , CHEMISTRY@ccl.net Message-id: <3BF28027.7241.1A6EDCDB@localhost> Organization: University College Dublin X-Mailer: Pegasus Mail for Win32 (v3.12c) Content-type: TEXT/PLAIN Priority: normal Date sent: Wed, 14 Nov 2001 07:16:46 -0500 From: Gary Breton Subject: CCL:Bonds vs No Bonds in Minimized Structures To: CHEMISTRY@ccl.net >Hello all, > >Is there any significance to the presence or absence of the bond? Why would >GaussView not put a bond into the structure? GaussView makes the call as to whether a bond exists based on the distance between the atoms in the archive entry or failing that the last geometry in the log file. Thus if the distance is slightly longer than gv expects for such a bond it is not shown. If you wish to present images of the converged structure with the bond present you can do this be selecting bond length on the builder panel, selecting the two atoms, and then clicking on the bond type button in the panel that opens. I hope this helps Laurence Cuffe > >Thanks and best regards! > > >Gary W. Breton >Chair and Associate Professor >Department of Chemistry >Berry College >PO Box 495016 >Mount Berry, GA 30149 > >"There's a light at the >end of the tunnel, but it >may be an oncoming train" > > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Wed Nov 14 10:17:38 2001 Received: from mail.laposte.net ([160.92.113.114]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAEFHbB24217 for ; Wed, 14 Nov 2001 10:17:38 -0500 Received: from nouveaupc (193.253.204.56) by mail.laposte.net (5.5.044) id 3BF14C590000DF38; Wed, 14 Nov 2001 16:17:21 +0100 Message-ID: <003b01c16d1f$b240f5e0$0b00000a@nouveaupc> From: "Alexandre Hocquet" To: "Gary Breton" , References: Subject: Re: CCL:Bonds vs No Bonds in Minimized Structures Date: Wed, 14 Nov 2001 16:18:43 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Looks like the GEOMETRICAL check used by Gaussview for existence or not of a N-N bond has a threshold between 1.45 and 1.49... Quantum mechanically, however, add or remove whatever bond you like : as long as you have the same nuclei in the same geometrical position with the same number of electrons, it will change nothing : the concept of bond is useless for the quantum mechanical molecule. The question "is there a bond between these two atoms" is thus not a straightforward one, and certainly geometry is a piece of information but rather incomplete. The analysis of the topology of the electronic density (AIM or Bader's theory) may also provide clues, but it is not the unique way either... We could even say that Molecular Mechanics, on the contrary, is a theory completely submitted to the concept of "bonding", because "bonding" is central to the definition of the energy (every energy term is defined with respect to "bound atoms"), hence the limitations with reactivity : you just can't break the bonds ! ------------------------------------------------------------ Alexandre HOCQUET Laboratoire de Physicochimie Biomoléculaire et Cellulaire ESA CNRS 7033 hocquet@lpbc.jussieu.fr Fax: 33 1 44277560 LPBC, case courrier 138 4 Place Jussieu, 75252 PARIS Cedex 05 France ------------------------------------------------------------ From chemistry-request@server.ccl.net Wed Nov 14 09:38:39 2001 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAEEcdB23159 for ; Wed, 14 Nov 2001 09:38:39 -0500 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id JAA15675; Wed, 14 Nov 2001 09:38:32 -0500 (EST) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Wed, 14 Nov 2001 09:38:02 -0500 (Eastern Standard Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GMS00AFDOFN3R@lvlmail.unitedcatalysts.com>; Wed, 14 Nov 2001 09:33:23 -0500 (EST) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Wed, 14 Nov 2001 09:38:16 -0500 Content-return: allowed Date: Wed, 14 Nov 2001 09:38:12 -0500 From: "Shobe, Dave" Subject: RE: Bonds vs No Bonds in Minimized Structures To: "'Gary Breton'" , CHEMISTRY@ccl.net Message-id: <157A51F55AAAD3119CD70008C7B1629D01C156FD@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) 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 fAEEcdB23160 I would not consider Gaussview's display or non-display of a bond as having ANY significance. I think there is a distance cutoff below which the two atoms are considered to be "bonded", probably based on covalent radii or something like that. --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: Gary Breton [mailto:gbreton@berry.edu] Sent: Wednesday, November 14, 2001 7:17 AM To: CHEMISTRY@ccl.net Subject: CCL:Bonds vs No Bonds in Minimized Structures Hello all, I have been conducting some geometry minimizations on some 1,2-diazacyclobutane structures using Gaussian98 with the GaussView GUI. When I minimize the parent compound (1,2-diazacyclobutane with N-H bonds) at the RHF631G* level, everything looks fine. If, however, I minimize at the RB3LYP6311+G** level, a similar structure to the HF minimization results, but GaussView does NOT SHOW a bond between the two nitrogen atoms. The bond has apparently not broken since the molecule adopts a geometry as if its still there (i.e., in the HF minimization the N-N, C-N and C-C bond lengths are 1.45405, 1.47272 and 1.53174, respectively, while in the B3LYP they are 1.49052, 1.49351 and 1.53844, respectively). Furthermore, if I start with the HF structure and further minimize at the B3LYP level, the bond again disappears! If I start with the B3LYP structure and ADD a N-N bond and then re-minimize, it again eliminates the bond. Is there any significance to the presence or absence of the bond? Why would GaussView not put a bond into the structure? Thanks and best regards! Gary W. Breton Chair and Associate Professor Department of Chemistry Berry College PO Box 495016 Mount Berry, GA 30149 "There's a light at the end of the tunnel, but it may be an oncoming train" -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Wed Nov 14 13:08:21 2001 Received: from hermes.bmc.uu.se ([130.238.39.245]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAEI8KB28596 for ; Wed, 14 Nov 2001 13:08:20 -0500 Received: from XRAY.bmc.uu.se ([130.238.37.10]) by hermes.bmc.uu.se (Post.Office MTA v3.5.3 release 223 ID# 0-62649U1500L1000S0V35) with ESMTP id se; Wed, 14 Nov 2001 19:08:07 +0100 Received: from zorn.bmc.uu.se (IDENT:spoel@zorn.bmc.uu.se [130.238.37.95]) by XRAY.bmc.uu.se (8.9.3/8.8.7) with ESMTP id TAA20233; Wed, 14 Nov 2001 19:10:41 +0100 Date: Wed, 14 Nov 2001 19:07:57 +0100 (CET) From: David van der Spoel X-Sender: spoel@zorn.bmc.uu.se To: David Smith cc: CCL Subject: Re: CCL:creating pdbs In-Reply-To: <3BF291B2.6DA7C211@mindless.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 14 Nov 2001, David Smith wrote: >Hello all, > >Does anyone know of a free program (linux/windows) which can create (or >edit) small molecule pdb files. I've looked at many programs but have >found none. Thanks for all suggestions. There's a webserver that gives you even a minimized conformation if you just draw the structure http://davapc1.bioch.dundee.ac.uk/programs/prodrg/prodrg.html Just paste in something like H-N-C=O | H And you get the correct molecule including missing hydrogens. Groeten, David. ________________________________________________________________________ Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry Husargatan 3, Box 576, 75123 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel@xray.bmc.uu.se spoel@gromacs.org http://zorn.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Wed Nov 14 13:20:54 2001 Received: from mcmail.cis.mcmaster.ca (mattacf@[130.113.64.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAEIKsB28926 for ; Wed, 14 Nov 2001 13:20:54 -0500 Received: from localhost (mattacf@localhost) by mcmail.cis.mcmaster.ca with ESMTP id NAA22087; Wed, 14 Nov 2001 13:20:14 -0500 (EST) Date: Wed, 14 Nov 2001 13:20:14 -0500 (EST) From: "C.F. Matta" To: Alexandre Hocquet cc: Gary Breton , Subject: Re: CCL:Bonds vs No Bonds in Minimized Structures In-Reply-To: <003b01c16d1f$b240f5e0$0b00000a@nouveaupc> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Alexandre On Wed, 14 Nov 2001, Alexandre Hocquet wrote: > The question "is there a bond between these two atoms" is thus not a > straightforward one, and certainly geometry is a piece of information but > rather incomplete. The analysis of the topology of the electronic density > (AIM or Bader's theory) may also provide clues, but it is not the unique way I partially agree with you. We have just published a paper which shows how the bond path, a line of maximum density linking two nuclei mirrored by a line of maximal stabilization in space (maximlly negative potential energy density), provides a unique answer to the question of whether bonding exists or not. We use an example from experiment where distance alone gives an ambiguous picture while the bond path provides a clear cut answer accompagnied by a host of other consequences. For instance, we find significantly higher electron delocalization between two bonded atoms (sharing a bond path) than between similar atoms separated by the same distance but whithout sharing a bond path: See: ==== Bader, R.F.W.; Matta, C.F. "Bonding to Titanium", Inorg. Chem. (2001), 40, 5603-5611. Also see: ========= Bader, R.F.W."A Bond Path: A Universal Indicator of Bonded Interaction", J. Phys. Chem. A (1998), 102, 7314-7323. Best wishes, Cherif ___________________________________________________________________________ Cherif F. Matta tel. (905) 525-9140 ext. 22502 Chemistry Department fax (905) 522-2509 McMaster University Hamilton, Ontario, CANADA L8S 4M1. ___________________________________________________________________________ From chemistry-request@server.ccl.net Wed Nov 14 15:05:13 2001 Received: from postal.sdsc.edu (IDENT:ChZJcbbvksCa3Zs13637P2fmjZ1bpF79@[132.249.20.114]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAEK5DB31447 for ; Wed, 14 Nov 2001 15:05:13 -0500 Received: from koa.sdsc.edu (IDENT:9U8K36RiHqSdXLhMq/DyCR0k4gAkf98O@koa.sdsc.edu [132.249.23.116]) by postal.sdsc.edu (8.11.6/8.11.6/SDSCserver-20) with ESMTP id fAEK54j14277; Wed, 14 Nov 2001 12:05:04 -0800 (PST) Received: from localhost by koa.sdsc.edu (SGI-8.9.3/1.11-IRIXclient) with ESMTP id MAA58500; Wed, 14 Nov 2001 12:05:04 -0800 (PST) Date: Wed, 14 Nov 2001 12:05:03 -0800 From: Wibke Sudholt To: Martijn Zwijnenburg cc: Subject: Re: CCL:solvent models in G98, comparison In-Reply-To: <3BF258A8.7617.5FCDAB@localhost> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, for an extensive overview about reaction field solvation models, take a look at: C. J. Cramer, D. G. Truhlar, Chem. Rev. 99 (1999) 2161 and reviews/references cited therein. Hopefully this helps! Best regards, Wibke Sudholt University of California, San Diego wibke@sdsc.edu On Wed, 14 Nov 2001, Martijn Zwijnenburg wrote: > Dear all, > > I'm very interested in calculating solution properties of molecules > by means of SCRF in Gaussian 98. However, there are various > models and I'm not sure of there merits. I've looked through the > literature but have been unable to find a review article comparing > the different methods. Does somebody know where to find such an > article?? > > Gr. Martijn > ------------------------------------------------------------------------- > Martijn Zwijnenburg > Lab. of Applied Organic Chemistry and Catalysis > Delft University of Technology > Julianalaan 136 > 2628 BL Delft > The Netherlands > Tel: 0031-(0)152782691 > Fax: 0031-(0)152784700 > e-mail: M.A.Zwijnenburg@tnw.tudelft.nl > web page: http://come.to/tock > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Wed Nov 14 15:21:57 2001 Received: from biomath.nyu.edu ([128.122.250.118]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAEKLvB31831 for ; Wed, 14 Nov 2001 15:21:57 -0500 Received: from tiberias.biomath.nyu.edu (tiberias.biomath.nyu.edu [128.122.250.87]) by biomath.nyu.edu (8.9.3/8.9.3) with ESMTP id PAA758283; Wed, 14 Nov 2001 15:20:58 -0500 (EST) Date: Wed, 14 Nov 2001 15:22:47 -0500 From: Linjing Yang Reply-To: Linjing Yang To: cc: Subject: parameters for 5'-phosphate GUA Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I am wondering if anybody knows the AMBER parameters and atom charges for the following DNA residue of 5'-terminal phosphate GUA: O1P H5' H4' O4' dG | | \ / \ / H5T-O5T--P-O5'-C5'---C4' C1' | | \ / \ O2P H5'' C3'--C2' H1' / \ / \ O3' H3'H2' H2'' | In addition, which atom type should O5T belongs to, OH or O2? Thanks in advance. Linjing From chemistry-request@server.ccl.net Wed Nov 14 19:13:18 2001 Received: from qtp.ufl.edu ([128.227.89.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAF0DIB03642 for ; Wed, 14 Nov 2001 19:13:18 -0500 Received: from pc1 (pc1 [128.227.192.187]) by qtp.ufl.edu (8.9.1a/8.9.1) with SMTP id TAA15300; Wed, 14 Nov 2001 19:13:37 -0500 (EST) Message-ID: <000901c16d6b$1784c530$bbc0e380@qtp.ufl.edu> From: "Stefan Fau" To: "Gary Breton" Cc: "CCL - all" References: Subject: Re: CCL:Bonds vs No Bonds in Minimized Structures Date: Wed, 14 Nov 2001 11:49:23 -0500 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 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Dear Prof. Breton, Dr. Robinson is right. Most viewing programs do not analyze the electronic structure to determine if there is a bond between two atoms. Instead they may compare the distance to the sum of covalent radii or look if the input file specifies the existence of a bond between the atoms in question (molecular mechanics). I assume that GaussView uses the distance criterion. Since the covalent radius of N is 0.74A, the NN distances in your molecule are near the critical distance for drawing a bond or not. You may analyze the electronic structure of your molecules with Bader's AIM method or Weinholds NBO analysis. AIM analyzes the topography of the electron density and defines a bond as a line connecting two atoms that is a maximum of the electron density in the planes orthogonal to each of its points. The NBO analysis is a series of basis set transformations that results in the best "Lewis structure". Each NBO corresponds to a line (or lone pair) in a Lewis structure. NBO finds the best resonance structure. It does not necessarily find NBOs that preserve the molecular symmetry (e.g. benzene). Stefan ______________________________________________________________________ Dr. Stefan Fau | fau@qtp.ufl.edu Quantum Theory Project | (352) 392-6714 University of Florida Gainesville, FL 32611-8435 From chemistry-request@server.ccl.net Wed Nov 14 16:39:02 2001 Received: from femail45.sdc1.sfba.home.com ([24.254.60.39]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAELd1B01361 for ; Wed, 14 Nov 2001 16:39:01 -0500 Received: from C1353359A ([65.4.172.51]) by femail45.sdc1.sfba.home.com (InterMail vM.4.01.03.20 201-229-121-120-20010223) with SMTP id <20011114213848.JWGT19618.femail45.sdc1.sfba.home.com@C1353359A>; Wed, 14 Nov 2001 13:38:48 -0800 Message-ID: <007b01c16d54$43649430$33ac0441@sttln1.wa.home.com> Reply-To: "Mark A. Thompson" From: "Mark A. Thompson" To: "David van der Spoel" , "David Smith" Cc: "CCL" References: Subject: Re: CCL:creating pdbs Date: Wed, 14 Nov 2001 13:35:21 -0800 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 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 ArgusLab (http://www.planaria-software.com) runs on Windows and will do almost everything you want (version 2 does not write pdb files but will read them; (version 3 will write pdb files)). Mark Thompson > On Wed, 14 Nov 2001, David Smith wrote: > > >Hello all, > > > >Does anyone know of a free program (linux/windows) which can create (or > >edit) small molecule pdb files. I've looked at many programs but have From chemistry-request@server.ccl.net Wed Nov 14 21:20:41 2001 Received: from smtp.dicp.ac.cn ([159.226.159.50]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAF2KeB04950 for ; Wed, 14 Nov 2001 21:20:40 -0500 Received: from congyao ([159.226.159.204]) by smtp.dicp.ac.cn (8.11.6/8.11.6) with SMTP id fAF2KWd09657 for ; Thu, 15 Nov 2001 10:20:32 +0800 Message-Id: <200111150220.fAF2KWd09657@smtp.dicp.ac.cn> Date: Thu, 15 Nov 2001 10:20:17 +0800 From: wangyanemail To: "CHEMISTRY@ccl.net" Subject: about calculating frequency in Dmol3 X-mailer: FoxMail 3.11 Release [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Dear CCLers I have a question about calculating frequency in Dmol3. Now ,when I calculate frequency of a model which is large ,it always calculate all frequency. It take much time. But I am only interested in a frequency between two atoms, how should I do . Thanks in advance. wangyanemail wangyanemail@dicp.ac.cn From chemistry-request@server.ccl.net Wed Nov 14 21:37:13 2001 Received: from postal.sdsc.edu (IDENT:zP9E135QrQptDTSvkE248xi+VCMSxhri@[132.249.20.114]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAF2bDB05105 for ; Wed, 14 Nov 2001 21:37:13 -0500 Received: from koa.sdsc.edu (IDENT:oDUOs9/oP395E4YYSSoVfuXt7W9RDhzB@koa.sdsc.edu [132.249.23.116]) by postal.sdsc.edu (8.11.6/8.11.6/SDSCserver-20) with ESMTP id fAF2b5j20420 for ; Wed, 14 Nov 2001 18:37:05 -0800 (PST) Received: from localhost by koa.sdsc.edu (SGI-8.9.3/1.11-IRIXclient) with ESMTP id SAA59537; Wed, 14 Nov 2001 18:37:04 -0800 (PST) Date: Wed, 14 Nov 2001 18:37:04 -0800 From: Wibke Sudholt To: Subject: Re: CCL:Bonds vs No Bonds in Minimized Structures In-Reply-To: <000901c16d6b$1784c530$bbc0e380@qtp.ufl.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, first of all I have to excuse that I did not follow the whole discussion. I only would like to add (if not already done) the ELF (electron localization function) concept to the methods to analyse chemical bonds. Best regards, Wibke Sudholt University of California, San Diego