From owner-chemistry@ccl.net Sun Apr 6 04:14:01 2008 From: "Arvydas Tamulis tamulis_._mserv.itpa.lt" To: CCL Subject: CCL: How to insert methanol solvent in Turbomole COSMO? Message-Id: <-36648-080406040931-4167-hx4LfQuH6hy8o2OB5JKhww(0)server.ccl.net> X-Original-From: Arvydas Tamulis Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Sun, 6 Apr 2008 10:34:39 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Arvydas Tamulis [tamulis^mserv.itpa.lt] Dear Colleagues, I have calculated successfully spectrum of the [Ru(bpy)3]2+ in vacuum by Turbomole but I do not know how to calculate [Ru(bpy)3]2+ in methanol solvent cavity by using COSMO? I am trying to use cosmoprep utility. I accept all default values in it, just make "r all o" to optimize radius. And then cosmoprep exist. I can't find a way to specify a solvent (methanol) atoms. How I can do it ? With best regards, Arvydas Tamulis From owner-chemistry@ccl.net Sun Apr 6 04:48:01 2008 From: "Andreas Bender, PhD Andreas.Bender^_^cantab.net" To: CCL Subject: CCL: Original reference for Tanimoto similarity Message-Id: <-36649-080406042911-10941-SgOtoplVBBcb3k/rwMjEJg*|*server.ccl.net> X-Original-From: "Andreas Bender, PhD" Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 6 Apr 2008 09:33:41 +0200 MIME-Version: 1.0 Sent to CCL by: "Andreas Bender, PhD" [Andreas.Bender,+,cantab.net] Hi Willem, > From what I am aware of (I was revising the area quite a lot for my recent PhD thesis) what we call now the 'Tanimoto' Coefficient was originally published by Paul Jaccard in 1901 with the intention to compare ecosystems - more precisely the types of flowers present in the basin of a certain river, with those types of flowers present in adjacent regions[1]. Accordingly, in some publications the coefficient is referred to as the 'Jaccard-Tanimoto' coefficient (or simply the Jaccard coefficient) and this is the earliest reference I could find which employs what we call now the 'Tanimoto' coefficient. As for the first reference by Taffee Tanimoto himself, usually an internal report at IBM is given [2] (such as in the overview of similarity coefficients at Daylight at http://www.daylight.com/dayhtml/doc/theory/theory.finger.html) but I couldn't get hold of this paper yet. Closely related, and I found that really interesting to read, was a paper by Amos Tversky on the human perception of similarities based on individual features [3]. In this work Tversky also provides a theoretical foundation for more unusual similarity coefficients such as asymmetrical coefficients, all based on human psychology but also with implications for molecular similarity searching. Since molecular similarity (as well as any other similarity) is a highly subjective area, the Tversky work is of course not able to "solve" problems associated with feature-based similarities, but it outlines the implicit assumptions behind similarity measured via features and coefficients in a very clear manner so I can recommend that work to anyone interested in similarity measures. If you can't get hold of the journal please just contact me and I would of course be very happy to provide you with a reprint. All the best, Andreas [1] P. Jaccard, 1901, Distribution de la flore alpine dans le bassin des Dranses et dans quelques r=E9gions voisines. Bulletin del la Soci=E9t= =E9 Vaudoise des Sciences Naturelles 37, 241-272. [2] T.T. Tanimoto, 1957, IBM Internal Report 17th Nov. [3] A. Tversky, 1977, Features of similarity. Psychological Review, 84(4), 327-352 --=20 Andreas Bender, PhD, Assistant Professor for Cheminformatics Leiden / Amsterdam Center for Drug Research Pharma-IT Platform: http://www.pharma-it.net Division of Medicinal Chemistry: http://www.medchem.leidenuniv.nl Personal Homepage: http://www.andreasbender.de On Sat, Apr 5, 2008 at 11:58 PM, Willem van Hoorn willem.van.hoorn^pfizer.com wrote: > > Sent to CCL by: "Willem van Hoorn" [willem.van.hoorn~!~pfizer.com] > Hello, > > The Tanimoto coefficient is bread and butter for 2D chemical similarity = searches but does anyone know the original publication? The reference below= is as close as I could get. > > A Computer Program for Classifying Plants > David J. Rogers and Taffee T. Tanimoto > http://www.sciencemag.org/cgi/content/citation/132/3434/1115 > > Thanks, > > Willem van Hoorn > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: search= )> > > From owner-chemistry@ccl.net Sun Apr 6 10:33:00 2008 From: "Soren Eustis soren[*]jhu.edu" To: CCL Subject: CCL: opening linux (64-bit) genereated .chk files on PC (revisited) Message-Id: <-36650-080406103132-10354-NwXtTS/cWcuCtGjinEy0/g * server.ccl.net> X-Original-From: "Soren Eustis" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_0007_01C897D1.55CEBBB0" Date: Sun, 6 Apr 2008 10:31:11 -0400 MIME-Version: 1.0 Sent to CCL by: "Soren Eustis" [soren.+*+.jhu.edu] This is a multipart message in MIME format. ------=_NextPart_000_0007_01C897D1.55CEBBB0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit I received some responses to my earlier inquiry regarding a problem I am having visualizing and/or reading .chk files generated on a linux 64-bit system with a windows 32-bit system. So far, the problem remains, and I am hoping someone else may have some ideas. Basically, I go through the process of converting from unix to DOS (using todos or unix2dos), then trying to run the fchk utility. I have also tried simply opening the file using gview03 directly at various stages of the process to no avail. Here is an output: C:\Users\Soren\Desktop>todos cysteineadiff.chk C:\Users\Soren\Desktop>formchk cysteineadiff Bad file opened by FileIO: Unit=2 I= 2 FPrev=40448 FCur= 0. FileIO: IOper= 9 IFilNo(1)= 2 Len= 0 IPos= 0 Q= 4476372 Error termination in NtrErr: NtrErr Called from FileIO. Thus, it seems this is larger than a simple unix/dos issue. Any ideas?? Thanks in advance. Soren N. Eustis Doctoral Candidate Department of Chemistry Johns Hopkins University 3400 N. Charles Street Baltimore, MD 21218 (W) 410-516-4675 (M) 410-925-5167 (fax) 410-516-8420 soren+*+jhu.edu ------=_NextPart_000_0007_01C897D1.55CEBBB0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

I received some responses to my earlier inquiry = regarding a problem I am having visualizing and/or reading .chk files generated on a = linux 64-bit system with a windows 32-bit system.  So far, the problem remains, = and I am hoping someone else may have some ideas.

 

Basically, I go through the process of converting = > from unix to DOS (using todos or unix2dos), then trying to run the fchk = utility.  I have also tried simply opening the file using gview03 directly at various = stages of the process to no avail.  Here is an output:

 

 

C:\Users\Soren\Desktop>todos = cysteineadiff.chk

 

C:\Users\Soren\Desktop>formchk = cysteineadiff

 Bad file opened by FileIO:  Unit=3D2 = I=3D  2 FPrev=3D40448 FCur=3D    0.

FileIO: IOper=3D 9 = IFilNo(1)=3D     2 = Len=3D           0 IPos=3D           0 = Q=3D

 4476372

 Error termination in NtrErr:

 NtrErr Called from FileIO.

 

 

Thus, it seems this is larger than a simple = unix/dos issue.  Any ideas??

 

Thanks in advance.

 

Soren N. Eustis

Doctoral Candidate

Department of Chemistry

Johns Hopkins University

3400 N. Charles Street

Baltimore, MD 21218

(W) 410-516-4675

(M) 410-925-5167

(fax) 410-516-8420

soren+*+jhu.edu

 

------=_NextPart_000_0007_01C897D1.55CEBBB0-- From owner-chemistry@ccl.net Sun Apr 6 13:57:01 2008 From: "Soren Eustis soren*o*jhu.edu" To: CCL Subject: CCL: opening linux (64-bit) genereated .chk files on PC (revisited) Message-Id: <-36651-080406134852-25357-fiEbAZGe9n//KFifYUHeUg-$-server.ccl.net> X-Original-From: "Soren Eustis" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Sun, 6 Apr 2008 12:48:34 -0400 MIME-Version: 1.0 Sent to CCL by: "Soren Eustis" [soren.:.jhu.edu] Joseph, Many thanks. That did the trick. Soren -----Original Message----- > From: Joseph Han [mailto:jhh3851!A!yahoo.com] Sent: Sunday, April 06, 2008 11:04 AM To: CCL Subscribers; soren!A!jhu.edu Subject: Re: CCL: opening linux (64-bit) genereated .chk files on PC (revisited) Soren, You should *NOT* run todos or unix2dos on the .chk file. The .chk file is a binary file and doing the conversion likely corrupts the file and may lead to the errors which you are experiencing. If possible, you should run formchk on the machine which generated the .chk file. Then transfer the .fchk file to the Windows machine. In this case, you *MAY* need to run unix2dos or todos on the .fchk file, but in most cases, I have found that it is not necessary. Joseph --- "Soren Eustis soren[*]jhu.edu" wrote: > I received some responses to my earlier inquiry regarding a problem I am > having visualizing and/or reading .chk files generated on a linux 64-bit > system with a windows 32-bit system. So far, the problem remains, and I am > hoping someone else may have some ideas. > > > > Basically, I go through the process of converting from unix to DOS (using > todos or unix2dos), then trying to run the fchk utility. I have also tried > simply opening the file using gview03 directly at various stages of the > process to no avail. Here is an output: > > > > > > C:\Users\Soren\Desktop>todos cysteineadiff.chk > > > > C:\Users\Soren\Desktop>formchk cysteineadiff > > Bad file opened by FileIO: Unit=2 I= 2 FPrev=40448 FCur= 0. > > FileIO: IOper= 9 IFilNo(1)= 2 Len= 0 IPos= 0 Q= > > 4476372 > > Error termination in NtrErr: > > NtrErr Called from FileIO. > > > > > > Thus, it seems this is larger than a simple unix/dos issue. Any ideas?? > > > > Thanks in advance. > > > > Soren N. Eustis > > Doctoral Candidate > > Department of Chemistry > > Johns Hopkins University > > 3400 N. Charles Street > > Baltimore, MD 21218 > > (W) 410-516-4675 > > (M) 410-925-5167 > > (fax) 410-516-8420 > > soren|jhu.edu > > > > From owner-chemistry@ccl.net Sun Apr 6 15:50:00 2008 From: "Joseph Han jhh3851%x%yahoo.com" To: CCL Subject: CCL: opening linux (64-bit) genereated .chk files on PC (revisited) Message-Id: <-36652-080406120427-12773-cR15Ew3vlUy1Ij69p0eJug(a)server.ccl.net> X-Original-From: Joseph Han Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Sun, 6 Apr 2008 08:04:15 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Joseph Han [jhh3851%a%yahoo.com] Soren, You should *NOT* run todos or unix2dos on the .chk file. The .chk file is a binary file and doing the conversion likely corrupts the file and may lead to the errors which you are experiencing. If possible, you should run formchk on the machine which generated the .chk file. Then transfer the .fchk file to the Windows machine. In this case, you *MAY* need to run unix2dos or todos on the .fchk file, but in most cases, I have found that it is not necessary. Joseph --- "Soren Eustis soren[*]jhu.edu" wrote: > I received some responses to my earlier inquiry regarding a problem I am > having visualizing and/or reading .chk files generated on a linux 64-bit > system with a windows 32-bit system. So far, the problem remains, and I am > hoping someone else may have some ideas. > > > > Basically, I go through the process of converting from unix to DOS (using > todos or unix2dos), then trying to run the fchk utility. I have also tried > simply opening the file using gview03 directly at various stages of the > process to no avail. Here is an output: > > > > > > C:\Users\Soren\Desktop>todos cysteineadiff.chk > > > > C:\Users\Soren\Desktop>formchk cysteineadiff > > Bad file opened by FileIO: Unit=2 I= 2 FPrev=40448 FCur= 0. > > FileIO: IOper= 9 IFilNo(1)= 2 Len= 0 IPos= 0 Q= > > 4476372 > > Error termination in NtrErr: > > NtrErr Called from FileIO. > > > > > > Thus, it seems this is larger than a simple unix/dos issue. Any ideas?? > > > > Thanks in advance. > > > > Soren N. Eustis > > Doctoral Candidate > > Department of Chemistry > > Johns Hopkins University > > 3400 N. Charles Street > > Baltimore, MD 21218 > > (W) 410-516-4675 > > (M) 410-925-5167 > > (fax) 410-516-8420 > > soren|jhu.edu > > > > From owner-chemistry@ccl.net Sun Apr 6 18:12:01 2008 From: "Mariusz Radon mariusz.radon-x-gmail.com" To: CCL Subject: CCL: How to insert methanol solvent in Turbomole COSMO? Message-Id: <-36653-080406173511-31394-Udbot1UbJ9GJBN9h/1Aj1g * server.ccl.net> X-Original-From: Mariusz Radon Content-Type: text/plain; charset=us-ascii Date: Sun, 06 Apr 2008 22:51:35 +0200 MIME-Version: 1.0 Sent to CCL by: Mariusz Radon [mariusz.radon()gmail.com] Dear Arvydas, What do you mean by ``solvent atoms''? > I can't find a way to specify a solvent (methanol) atoms. http://www.turbomole-gmbh.com/manuals/version_5_9/DOK_HTML/node253.html#21382 AFAIK, in COSMO you specify the solvent _solely_ by its dielectric permitivity (epsilon) and ``effective radius'' (rsolv), and several less important parameters to control cavity construction. regards, Mariusz Radon -- Mariusz Radon Department of Theoretical Chemistry Jagiellonian University mradon /at/ chemia.uj.edu.pl http://www.chemia.uj.edu.pl/~mradon