From owner-chemistry@ccl.net Mon May 22 04:10:01 2006 From: "D.BIO- Gerard Pujadas gerard.pujadas(_)urv.cat" To: CCL Subject: CCL: AutoDock's parameters for cooper? Message-Id: <-31801-060522040357-20437-te7fFhUSIj947bS90MeKBQ(a)server.ccl.net> X-Original-From: "D.BIO- Gerard Pujadas" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" Date: Mon, 22 May 2006 10:03:19 +0200 Mime-Version: 1.0 Sent to CCL by: "D.BIO- Gerard Pujadas" [gerard.pujadas]~[urv.cat] Dear Liviu, > >Hi all, >Related to Gerard's question, I am also >interested in finding out where would one find >the >parameters for Fe to be used in Autodock. I am >interested mainly in non-heme iron systems, >although the Fe parameters for heme systems may be a good start. >Thanks, you will find these values in the dist305/share/gpf3gen.awk file of your AutoDock directory: Rij[ "lj" "f" "f" ] = 1.30 # Fe-Fe epsij[ "lj" "f" "f" ] = 0.0100 * FE_vdW_coeff # Fe-Fe simply write: grep 'Fe-Fe' gpf3gen.awk > from a terminal when you were in the dist305/share/ directory Gerard -- ============================= NOTE: NEW E-MAIL ============================ Dr. Gerard Pujadas Grup de recerca en Nutrigenòmica Dept. Bioquímica i Biotecnologia room 106 Campus de Sant Pere Sescelades e-mail: gerard.pujadas]*[urv.cat Univ. Rovira i Virgili phone: 34-977 559565 C/ Marcel·lí Domingo fax: 34-977 558232 43007 Tarragona (CATALONIA) State: Spain (European Union) =========================================================================== From owner-chemistry@ccl.net Mon May 22 08:32:00 2006 From: "Silviu Zilberman silviu]_[Princeton.EDU" To: CCL Subject: CCL:G: EPR g-tensor with Gaussian Message-Id: <-31802-060522082658-1144-s8GnYuPjs9hoPW+DDRCnkg-x-server.ccl.net> X-Original-From: Silviu Zilberman Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 22 May 2006 15:26:06 +0200 MIME-Version: 1.0 Sent to CCL by: Silviu Zilberman [silviu]~[Princeton.EDU] Dear All, I would like to do some calculations of EPR g-tensor with Gaussian03, for some Fe complexes. I found the Gaussian manual somewhat unclear. It states that using Prop EPR one can get the hyperfine coupling constants, but it's not clear to me how to get the g-tensor. I would like to know what are the keywords and options that control the EPR g-tensor calculation. In addition I would appreciate comments on the proper basis set for these calculations? I found basis sets called EPR-II and EPR-III, which sound like a natural choice. Are these basis sets suitable for Fe complexes? Thanks, Silviu. From owner-chemistry@ccl.net Mon May 22 11:47:00 2006 From: "Frank Neese neese{=}thch.uni-bonn.de" To: CCL Subject: CCL: EPR g-tensor with Gaussian Message-Id: <-31803-060522110818-3737-jaDlxevauyvYWopdOmA6fA.@.server.ccl.net> X-Original-From: Frank Neese Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1"; format=flowed Date: Mon, 22 May 2006 16:07:56 +0200 Mime-Version: 1.0 Sent to CCL by: Frank Neese [neese[a]thch.uni-bonn.de] Dear Silviu, in case that you are adventourous enough to try another program i recommend the ORCA program to you for this purpose since it has been optimized for this type of application and also has an accurate spin orbit coupling treatment for such applications. It can be downloaded free of charge from http://ewww.mpi-muelheim.mpg.de/bac/index_en.php under "download area" proper basis set for these calculations? I found basis sets called >EPR-II and EPR-III, which sound like a natural choice. Are these basis >sets suitable for Fe complexes? ... they do not exist for Fe. THe basis sets of the Ahlrichs group (TZVP and higher) are suitable for g-tensor calculations. Best regards, Frank ---------------------------------------------------------------- Prof. Dr. Frank Neese Lehrstuhl für Theoretische Chemie Universität Bonn D-53115 Bonn e-mail: neese-$-thch.uni-bonn.de Tel.: 0228/732351 (secretary: Ms Kronz) FAX: 0228/739064 ---------------------------------------------------------------- From owner-chemistry@ccl.net Mon May 22 13:36:00 2006 From: "Victor Nemykin victor_nemykin]~[yahoo.com" To: CCL Subject: CCL:G: EPR g-tensor with Gaussian Message-Id: <-31804-060522124603-388-VuoLzDvpiTG3C5WXY7inMQ : server.ccl.net> X-Original-From: Victor Nemykin Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Mon, 22 May 2006 08:43:51 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Victor Nemykin [victor_nemykin*_*yahoo.com] Hello Silviu: You just need to add "nmr" to the Gaussian input line. As a result, you will have all g-tenzors printed in the NMR part of output file, while including "prop" keyword will allow you to get hyperfine coupling constants (both Fermi contact term and anisotropic part) in the "Properties" part of the output file. From the best of my knowledge, both EPR-II and EPR-III basis sets are not supporting Fe. I would recommend to use Wachter's basis set (from my experience "Wachter's+f" basis set gives a slightly better results as compared to "Wachter's" basis set, designated as 6-311+G, implimented into Gaussian) for the small-to-intermediate size molecules and DGauss DZVP basis set (designated as DGDZVP in Gaussian) for the intermediate-to-large size molecules. Next thing to worry about is uncontraction of the s-part of the basis set, which is (at least from my experience) bring a dramatic improvement of the calculated Fermi contact term values. Such uncontraction, however, comes with the computational cost: you have to use a better integration grid (i.e. Grid=250770) in order to avoid integration instability. Other than these suggestions, please have a look into Frank Neese's papers on calculation of the EPR parameters for numerous iron complexes. Best, Victor --- "Silviu Zilberman silviu]_[Princeton.EDU" wrote: > Sent to CCL by: Silviu Zilberman [silviu]~[Princeton.EDU] > Dear All, > > I would like to do some calculations of EPR g-tensor with Gaussian03, > > for some Fe complexes. I found the Gaussian manual somewhat unclear. > It > states that using Prop EPR one can get the hyperfine coupling > constants, > but it's not clear to me how to get the g-tensor. > > I would like to know what are the keywords and options that control > the > EPR g-tensor calculation. In addition I would appreciate comments on > the > proper basis set for these calculations? I found basis sets called > EPR-II and EPR-III, which sound like a natural choice. Are these > basis > sets suitable for Fe complexes? > > Thanks, Silviu. > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > > > ***** Dr. Victor N.Nemykin e-mail: victor_nemykin]![yahoo.com ***** __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Mon May 22 15:51:00 2006 From: "Charles McCallum mmccallum() pacific.edu" To: CCL Subject: CCL: Help with Mercury / defining a plane Message-Id: <-31805-060522154547-565-gJKokDZHWSap5rm98+rrIw- -server.ccl.net> X-Original-From: Charles McCallum Content-Type: multipart/alternative; boundary=Apple-Mail-1-366570671 Date: Mon, 22 May 2006 12:09:38 -0700 Mime-Version: 1.0 (Apple Message framework v750) Sent to CCL by: Charles McCallum [mmccallum|,|pacific.edu] --Apple-Mail-1-366570671 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed A colleague of mine is using the program Mercury (http:// www.ccdc.cam.ac.uk/products/csd_system/mercury/downloads/) to define some planes in her crystal structure, and while it is doing what she wants, it is not reporting an error/sum of residuals (or any other uncertainty). I know it is a long shot with this crowd, but does anyone have any experience with this? Either a way to extract this information from the program, or another program that would allow us to define planes including some atom selections, and give residuals would be most appreciated. Cheers, Mike -- C. Michael McCallum http://www.pacific.edu/college/ chemistry/McCallum/cmccallum.html Associate Professor Department of Chemistry, UOP mmccallum .at. pacific .dot. edu (209) 946-2636 v / (209) 946-2607 fax --Apple-Mail-1-366570671 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 A colleague of mine is using the = program Mercury (= http://www.ccdc.cam.ac.uk/products/csd_system/mercury/downloads/) to = define some planes in her crystal structure, and while it is doing what = she wants, it is not reporting an error/sum of residuals (or any other = uncertainty).=A0 I know it is a long shot with this crowd, but does = anyone have any experience with this?=A0 Either a way to extract this = information from the program, or another program that would allow us to = define planes including some atom selections, and give residuals would = be most appreciated.

Cheers,

Mike

=

C. Michael McCallum = =A0 =A0 =A0 = =A0 =A0 = http://www.pacific.edu/college/chemistry/McCallum/cmccallum.html

Associate Professor = =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0

=A0 = =A0

mmccallum .at. pacific .dot. = edu=A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 (209) 946-2636 v=A0 / (209) = 946-2607 fax


 =

= --Apple-Mail-1-366570671-- From owner-chemistry@ccl.net Mon May 22 16:49:00 2006 From: "Don Steiger sd00_2002]*[yahoo.com" To: CCL Subject: CCL: Clever parallel Fast Multipole Algorithms? Message-Id: <-31806-060522162303-18620-qise0Gz7URuEZlH9YOj19A],[server.ccl.net> X-Original-From: "Don Steiger" Date: Mon, 22 May 2006 16:23:00 -0400 Sent to CCL by: "Don Steiger" [sd00_2002(_)yahoo.com] I am looking for a parallel implementation of the FMM that has some clever (whatever that means) parallelization. Does anybody know of any implementation that uses some interesting, novel, or clever approach, idea, or logic to do the parallelization? From owner-chemistry@ccl.net Mon May 22 18:56:00 2006 From: "Mark William Jarvis Mark.Jarvis]![colorado.edu" To: CCL Subject: CCL: CBS calculations in Gaussian Message-Id: <-31807-060522183121-23178-5ntI5CsinuADGjqzj/Ti/Q_+_server.ccl.net> X-Original-From: Mark William Jarvis Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 22 May 2006 15:52:06 -0600 MIME-Version: 1.0 Sent to CCL by: Mark William Jarvis [Mark.Jarvis() colorado.edu] Hello, I am attempting a CBS energy calculation for 2-Phenethyl Phenyl Ether, C14H14O. As far as I know the job is set up properly and runs for just under 8 hours on a very fast computer. The DFT job finishes and then the CBS starts and then ends with these lines: Estimate disk for full transformation 7484901414 words. Semi-Direct transformation. ModeAB= 4 MOrb= 298 LenV= 102702660 LASXX= 1603627806 LTotXX= 2179233291 LenRXX= 2645088382 LTotAB= 465855091 MaxLAS= 1886244789 LenRXY= 0 NonZer= 3673110703 LenScr= 5531293696 LnRSAI= 3759872556 LnScr1= 7559372288 LExtra= 0 Total= 19495626922 MaxDsk= -1 SrtSym= T ITran= 5 Erroneous write. Write -1 instead of 4096. fd = 4 orig len = 4096 left = 4096 g_write I know I haven't run out of disk space, since the admin's did see any disk full messages. Has anyone emcountered this type of problem before? TIA Mark Jarvis Doctoral Candidate Department of Mechanical Engineering University of Colorado at Boulder From owner-chemistry@ccl.net Mon May 22 19:31:01 2006 From: "jaccos(!)ccdc.cam.ac.uk" To: CCL Subject: CCL: Help with Mercury / defining a plane Message-Id: <-31808-060522190200-27840-s21tyVqudIc83JyR6RYmCA###server.ccl.net> X-Original-From: jaccos_+_ccdc.cam.ac.uk Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Mon, 22 May 2006 23:03:29 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: jaccos%%ccdc.cam.ac.uk > Sent to CCL by: Charles McCallum [mmccallum|,|pacific.edu] > A colleague of mine is using the program Mercury (http:// > www.ccdc.cam.ac.uk/products/csd_system/mercury/downloads/) to define > some planes in her crystal structure, and while it is doing what she > wants, it is not reporting an error/sum of residuals (or any other > uncertainty). I know it is a long shot with this crowd, but does > anyone have any experience with this? Either a way to extract this > information from the program, or another program that would allow us > to define planes including some atom selections, and give residuals > would be most appreciated. As far as I can tell, this is indeed not possible with Mercury. I will pass your suggestion on to the Mercury developer for possible inclusion in a future release. Best wishes, -- Dr Jacco van de Streek Research Scientist Cambridge Crystallographic Data Centre Cambridge, United Kingdom From owner-chemistry@ccl.net Mon May 22 20:06:00 2006 From: "Liuming Yan yan.liuming.:.staff.shu.edu.cn" To: CCL Subject: CCL: Force field for Manganese and silicon Message-Id: <-31809-060522064758-23007-7XQA3kyJJ6E/9caoklREpQ^^^server.ccl.net> X-Original-From: "Liuming Yan" Content-Type: multipart/alternative; boundary="----=_Part_46667_769211.1148291417055" Date: Mon, 22 May 2006 17:50:17 +0800 MIME-Version: 1.0 Sent to CCL by: "Liuming Yan" [yan.liuming:-:staff.shu.edu.cn] ------=_Part_46667_769211.1148291417055 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear All, I try to simulate the system of manganese silicide using MD simulation, however, I can't find a force field parameter for Mn-Si. Does any one know who has simulated similar systems. Thanks! --=20 Dr. Liuming Yan Department of Chemistry Shanghai University 99 Shangda Road, Shanghai 200444, China, The People's Republic of Tele: 021-6613-2405 ------=_Part_46667_769211.1148291417055 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
Dear All,
 
I try to simulate the system of manganese silicide using MD simulation= , however, I can't find a force field parameter for Mn-Si. Does any one kno= w who has simulated similar systems.
 
Thanks!

--
Dr. Liuming Yan

Department = of Chemistry
Shanghai University
99 Shangda Road, Shanghai 200444,China, The People's Republic of
Tele: 021-6613-2405
------=_Part_46667_769211.1148291417055-- From owner-chemistry@ccl.net Mon May 22 20:41:01 2006 From: "Wayne Steinmetz WES04747^pomona.edu" To: CCL Subject: CCL: Help with Mercury / defining a plane Message-Id: <-31810-060522202719-9831-NHcid933ixUI3bG/c5mWig]-[server.ccl.net> X-Original-From: "Wayne Steinmetz" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 22 May 2006 17:26:57 -0700 MIME-Version: 1.0 Sent to CCL by: "Wayne Steinmetz" [WES04747(0)pomona.edu] Before I answer the question, I'll first summarize the task as I understand it. Given the three-dimensional structure of a molecule, one wishes to fit a set of atoms to a plane. For this purpose, I use a module in Tripos' SYBYL. SYBYL allows one to select the atoms by point-and-click or via a script written in SBYL Program language. The module generates an equation for the plane and the rms deviation of the atoms selected for the operation from the plane. The equation for the plane is added to the SYBYL mol2 file. One can in later operations calculate the distance of any atom in the structure from the plane. SYBYL uses a least-squares function to find the best plane for n atoms. Obviously, n must be at least 3. So the good news is the existence of the required functionality. The bad news is the price. Tripos has a budget program, Alchemy, which might have the required module. Wayne E. Steinmetz Carnegie Professor of Chemistry Woodbadge Course Director Chemistry Department Pomona College 645 North College Avenue Claremont, California 91711-6338 USA phone: 1-909-621-8447 FAX: 1-909-607-7726 Email: wsteinmetz,pomona.edu WWW: pages.pomona.edu/~wsteinmetz -----Original Message----- > From: owner-chemistry,ccl.net [mailto:owner-chemistry,ccl.net] Sent: Monday, May 22, 2006 12:00 PM To: Wayne Steinmetz Subject: CCL: Help with Mercury / defining a plane Sent to CCL by: Charles McCallum [mmccallum|,|pacific.edu] --Apple-Mail-1-366570671 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed A colleague of mine is using the program Mercury (http:// www.ccdc.cam.ac.uk/products/csd_system/mercury/downloads/) to define some planes in her crystal structure, and while it is doing what she wants, it is not reporting an error/sum of residuals (or any other uncertainty). I know it is a long shot with this crowd, but does anyone have any experience with this? Either a way to extract this information from the program, or another program that would allow us to define planes including some atom selections, and give residuals would be most appreciated. Cheers, Mike -- C. Michael McCallum http://www.pacific.edu/college/ chemistry/McCallum/cmccallum.html Associate Professor Department of Chemistry, UOP mmccallum .at. pacific .dot. edu (209) 946-2636 v / (209) 946-2607 fax --Apple-Mail-1-366570671 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 A colleague of mine is using the = program Mercury (= http://www.ccdc.cam.ac.uk/products/csd_system/mercury/downloads/) to = define some planes in her crystal structure, and while it is doing what = she wants, it is not reporting an error/sum of residuals (or any other = uncertainty).=A0 I know it is a long shot with this crowd, but does = anyone have any experience with this?=A0 Either a way to extract this = information from the program, or another program that would allow us to = define planes including some atom selections, and give residuals would = be most appreciated.

Cheers,

Mike

=

C. Michael McCallum = =A0 =A0 =A0 = =A0 =A0 = http://www.pacific.edu/college/chemistry/McCallum/cmccallum.html

Associate Professor = =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0

=A0 = =A0

mmccallum .at. pacific .dot. = edu=A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 (209) 946-2636 v=A0 / (209) = 946-2607 fax


 =

= --Apple-Mail-1-366570671--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt------------------------------------------------------------- This message has been scanned by Postini anti-virus software. From owner-chemistry@ccl.net Mon May 22 21:15:00 2006 From: "Ross Walker ross/./rosswalker.co.uk" To: CCL Subject: CCL: CBS calculations in Gaussian Message-Id: <-31811-060522203910-19067-QTFxv2D0Qumo+vtFwUoKQQ(_)server.ccl.net> X-Original-From: "Ross Walker" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Mon, 22 May 2006 17:38:59 -0700 MIME-Version: 1.0 Sent to CCL by: "Ross Walker" [ross+*+rosswalker.co.uk] Hi Mark, > Estimate disk for full transformation 7484901414 words. > Erroneous write. Write -1 instead of 4096. > I know I haven't run out of disk space, since the admin's did > see any disk full > messages. You probably have run out of disk space - or alternatively the code is trying to write a file that is too big for the system. E.g. you may only have a 32 bit system without large file access support enabled and then you would see this type of error. Note 7484901414 words is *8 = 59879211312 bytes = 55GB. So check you have >55 GB free. Plus that you don't have a quota and that you are running on a 64 bit machine or have compiled everything to allow you to write larger than 2GB files. All the best Ross /\ \/ |\oss Walker | HPC Consultant and Staff Scientist | | San Diego Supercomputer Center | | Tel: +1 858 822 0854 | EMail:- ross::rosswalker.co.uk | | http://www.rosswalker.co.uk | PGP Key available on request | Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues.