From owner-chemistry@ccl.net Mon Jan 4 01:49:01 2010 From: "Marcel Swart marcel.swart[]icrea.es" To: CCL Subject: CCL: pbepbe vs. tpsstpss Message-Id: <-40992-100103184617-24076-DMaBY7VuaJZ0VAMhiq/Tog,+,server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary=Apple-Mail-1-781820281 Date: Sun, 3 Jan 2010 23:14:21 +0100 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Marcel Swart [marcel.swart[a]icrea.es] --Apple-Mail-1-781820281 Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes Content-Transfer-Encoding: quoted-printable Even better is SSB-D. See: M. Swart, M. Sol=E0 and F.M. Bickelhaupt "A new all-round DFT functional based on spin states and SN2 barriers" J. Chem. Phys. 2009, 131, 094103 On Jan 3, 2010, at 7:34 AM, a b c ajohn1234[*]gmail.com wrote: > pbepbe versus tpsstpss > > which is better (esp. when it comes to an inorganic complex with an =20= > Fe metal center [say Fe(III) and/or Fe(II)])? > > thanks, > > anonymous grad student =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D dr. Marcel Swart ICREA Research Professor at Institut de Qu=EDmica Computacional Universitat de Girona Parc Cient=EDfic i Tecnol=F2gic Edifici Jaume Casademont (despatx A-27) Pic de Peguera 15 17003 Girona Catalunya (Spain) tel +34-972-183240 fax +34-972-183241 e-mail marcel.swart++icrea.es marcel.swart++udg.edu web http://www.marcelswart.eu =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D --Apple-Mail-1-781820281 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Even better is = SSB-D. See:

M. = Swart, M. Sol=E0 and F.M. Bickelhaupt
"A new all-round DFT functional = based on spin states and SN2 barriers"
J. Chem. = Phys. 2009, 131, = 094103

On Jan 3, 2010, = at 7:34 AM, a b c ajohn1234[*]gmail.com wrote:

pbepbe versus = tpsstpss

which is better (esp. when it comes to an inorganic = complex with an Fe metal center [say Fe(III) and/or = Fe(II)])?

thanks,

anonymous grad = student


=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

Institut de Qu=EDmica = Computacional
Universitat de Girona

Parc Cient=EDfic i = Tecnol=F2gic
Edifici Jaume Casademont (despatx = A-27)
Pic de Peguera 15
17003 Girona

+34-972-183240
fax
e-mail


= --Apple-Mail-1-781820281-- From owner-chemistry@ccl.net Mon Jan 4 05:24:01 2010 From: "Stan van Gisbergen vangisbergen-,-scm.com" To: CCL Subject: CCL: Treatments of symmetry in ground and excited states in current QM codes Message-Id: <-40993-100104044839-10080-gxIXHjLJ+AkdkT3+BChMdQ.@.server.ccl.net> X-Original-From: Stan van Gisbergen Content-Type: multipart/alternative; boundary=Apple-Mail-76-821109883 Date: Mon, 4 Jan 2010 10:09:11 +0100 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Stan van Gisbergen [vangisbergen..scm.com] --Apple-Mail-76-821109883 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Dear John, Best wishes for 2010 to you and other CCL subscribers. On Dec 28, 2009, at 5:58 PM, John McKelvey jmmckel=gmail.com wrote: > > Sent to CCL by: John McKelvey [jmmckel[*]gmail.com] > CCLers, > > What "ab initio"/DFT packages specify the symmetries of ground state > MO's, and according to irreducible representation allow specific > occupation of those MO's for the SCF process? In a geometry > optimization process? Using mean dielectric solvation? One possible answer is "ADF" to all the above. > What packages allow specification of excited states by symmetry? ADF An example input file that shows some of these features: http://www.scm.com/Doc/Doc2009.01/ADF/Examples/page82.html > Allow specific irreducible representation optimization of the excited > state geometry? Specific irreducible representation including the > refractive index? Allow excited state geometry optimization of a > specific irreducible representation including refractive index? Excited-state geometry optimization is not included in the current release, ADF2009. I'm afraid I'm not sure what you mean exactly by including refractive index. If you wish you can follow up off-line. Best regards, Stan Dr. S.J.A. van Gisbergen Scientific Computing & Modelling NV Theoretical Chemistry, Vrije Universiteit De Boelelaan 1083 1081 HV Amsterdam The Netherlands vangisbergen]![scm.com http://www.scm.com T: +31-20-5987626 F: +31-20-5987629 > > Best regards, > > John > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel]~[gmail.com > > > > -= 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/> > --Apple-Mail-76-821109883 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=US-ASCII Dear John, 

Best wishes for 2010 to you and = other CCL subscribers. 

On Dec 28, 2009, at = 5:58 PM, John McKelvey jmmckel=3Dgmail.com wrote:


Sent to = CCL by: John McKelvey [jmmckel[*]gmail.com]

What "ab initio"/DFT packages specify the symmetries = of ground state
MO's, and according to = irreducible representation allow specific
  In a geometry
optimization process?  Using mean dielectric = solvation?

One possible answer is = "ADF" to all the above.

What packages allow specification of excited states = by = symmetry?

ADF

An example input file that shows some of these features:

Allow specific irreducible = representation optimization of the excited
state = geometry?  Specific = irreducible representation including the
specific irreducible representation including = refractive index?

Excited-state = geometry optimization is not included in the current release, = ADF2009.
I'm afraid I'm not sure what you mean exactly by = including refractive index.
If you wish you can follow up = off-line. 

Best = regards,
Stan 

Dr. S.J.A. van Gisbergen
Scientific Computing & Modelling NV
Theoretical Chemistry, Vrije Universiteit
De Boelelaan 1083
1081 HV = Amsterdam
The Netherlands   =                     =          
T: +31-20-5987626    
F: +31-20-5987629




Best regards,

John

-- 
John McKelvey
10819 = Middleford Pl
Ft Wayne, IN 46818
260-489-2160


-=3D = This is automatically added to each message by the mailing script = =3D-
To recover the email address of = the author of the message, please change
the = strange characters on the top line to the ]![ sign. You can also
look up the X-Original-From: line in the mail = header.

E-mail to subscribers: CHEMISTRY]![ccl.net or = use:

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= --Apple-Mail-76-821109883-- From owner-chemistry@ccl.net Mon Jan 4 13:48:00 2010 From: "Andrew Voronkov drugdesign|a|yandex.ru" To: CCL Subject: CCL: I am looking for software which can compare chemical databases and select the same compounds into a separate dataset Message-Id: <-40994-100104092600-30021-8bfiS8nOZVYQF0AvdkhSyA|,|server.ccl.net> X-Original-From: Andrew Voronkov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Mon, 04 Jan 2010 16:56:07 +0300 MIME-Version: 1.0 Sent to CCL by: Andrew Voronkov [drugdesign(~)yandex.ru] Dear CCL users, I am looking for free or evaluation software which can analyse datasets of small molecules and select the intersections. For example I am making virtual screen through different biotargets and get let s say 5 datasets by 500 compounds. I want to select only potential multitarget compounds and select only compounds which are presented in all of the datasets. Is there software which can compare a number of datasets and create the resulted database containg the overlaping compounds? Sincerely yours, Andrew From owner-chemistry@ccl.net Mon Jan 4 15:11:01 2010 From: "Igor Filippov Contr igorf+*+helix.nih.gov" To: CCL Subject: CCL: I am looking for software which can compare chemical databases and select the same compounds into a separate dataset Message-Id: <-40995-100104150416-936-48W9KCwLwo8ihTM1VWrEAQ-#-server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="UTF-8" Date: Mon, 04 Jan 2010 15:04:38 -0500 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf*_*helix.nih.gov] Andrew, Any chemoinformatics toolkit can probably do this, but I would mention 3 that are the most representative IMHO: - PipelinePilot - very easy to use for a non-programmer, but could be somewhat expensive, - CACTVS - closed source, but free for academic use, it has an unmatched ability to fine tune what precisely do you mean as "identical" structures - as long as you're comfortable with its Tcl-derived API, - OpenBabel - free and open source! Regards, Igor On Mon, 2010-01-04 at 08:56 -0500, Andrew Voronkov drugdesign|a| yandex.ru wrote: > Sent to CCL by: Andrew Voronkov [drugdesign(~)yandex.ru] > Dear CCL users, > I am looking for free or evaluation software which can analyse datasets of small molecules and select the intersections. For example I am making virtual screen through different biotargets and get let s say 5 datasets by 500 compounds. I want to select only potential multitarget compounds and select only compounds which are presented in all of the datasets. Is there software which can compare a number of datasets and create the resulted database containg the overlaping compounds? > > > Sincerely yours, > Andrew> > From owner-chemistry@ccl.net Mon Jan 4 16:09:00 2010 From: "Andrew Orry andy:-:molsoft.com" To: CCL Subject: CCL: I am looking for software which can compare chemical databases and select the same compounds into a separate dataset Message-Id: <-40996-100104151838-4544-yKiin7jDsxV+2vDY7VhgTw/./server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 04 Jan 2010 11:17:02 -0800 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy]^[molsoft.com] Andrew, MolSoft's ICM-Chemist software can compare chemical databases and select the intersections - please see http://www.molsoft.com/icm-chemist.html There is a video example on how to compare datasets in our ICM-Chemist tutorial web page here http://www.molsoft.com/icm-chemist-tutorials.html We offer full feature evaluation licenses and competitive perpetual license pricing for this product. Thanks, -- Andrew Orry Ph.D. Senior Scientist MolSoft LLC 3366 North Torrey Pines Court Suite 300 La Jolla, CA 92037 U S A Phone: (858) 625-2000 (x108) Fax: (858) 625-2888 www.molsoft.com Latest ICM News: www.molsoft.com/news.html Andrew Voronkov drugdesign|a|yandex.ru wrote: > Sent to CCL by: Andrew Voronkov [drugdesign(~)yandex.ru] > Dear CCL users, > I am looking for free or evaluation software which can analyse datasets of small molecules and select the intersections. For example I am making virtual screen through different biotargets and get let s say 5 datasets by 500 compounds. I want to select only potential multitarget compounds and select only compounds which are presented in all of the datasets. Is there software which can compare a number of datasets and create the resulted database containg the overlaping compounds? > > > Sincerely yours, > Andrew> > From owner-chemistry@ccl.net Mon Jan 4 16:52:00 2010 From: "Wolf-D. Ihlenfeldt wdi..xemistry.com" To: CCL Subject: CCL: AW: I am looking for software which can compare chemical databases and select the same compounds into a separate dataset Message-Id: <-40997-100104162752-11138-OdixjIiI30XsIYGC4FyTvg/a\server.ccl.net> X-Original-From: "Wolf-D. Ihlenfeldt" Content-Language: de Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 4 Jan 2010 21:57:18 +0100 MIME-Version: 1.0 Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi * xemistry.com] > -----Urspr=FCngliche Nachricht----- > Von: owner-chemistry+wdi=3D=3Dxemistry.com#%#ccl.net [mailto:owner- > chemistry+wdi=3D=3Dxemistry.com#%#ccl.net] Im Auftrag von Andrew = Voronkov > drugdesign|a|yandex.ru > Gesendet: Montag, 4. Januar 2010 14:56 > An: Ihlenfeldt, Wolf D > Betreff: CCL: I am looking for software which can compare chemical > databases and select the same compounds into a separate dataset >=20 >=20 > Sent to CCL by: Andrew Voronkov [drugdesign(~)yandex.ru] > Dear CCL users, > I am looking for free or evaluation software which can analyse > datasets of small molecules and select the intersections. For example = I > am making virtual screen through different biotargets and get let s = say > 5 datasets by 500 compounds. I want to select only potential > multitarget compounds and select only compounds which are presented in > all of the datasets. Is there software which can compare a number of > datasets and create the resulted database containg the overlaping > compounds? >=20 Here is a straightforward (7 actual code lines) CACTVS script (www.xemistry.com, free for academics) script for this: --snip-- # open result file for writing set fhout [molfile open intersection.sdf w] # loop over files dataset_1.sdf dataset_5.sdf loop i 1 6 { set fh [molfile open dataset_$i.sdf] # loop over all records in the current file molfile hloop $fh eh { # count instances of structure hashcode (with stereo and isotope labels) # look whether hashcode was seen 5 times. OK, this = assumes we have # no same-file duplicate structures in the input = datafiles, but let's assume that is true for the sake of simplicity if {[incr hashes([ens get $eh E_HASHISY])]=3D=3D5} { molfile write $fhout $eh } } } molfile close all --snip-- The script only keeps structure hashcode refcounts in memory, besides = the current structure,=20 so there is virtually no limit on the sizes of the files you can check.=20 The sample code assumes the input and output are SD files with a = specific naming scheme, but it is simple to change this to any other desired = format. >=20 > Sincerely yours, > Andrew >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please > change>=20>=20>=20>=20>=20> Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20