On Jul 29, 2013, at 2:56 PM, Jose S ez = josesaez(a)uv.es wrote:

Sent to CCL by: "Jose S ez" = [josesaez]|[uv.es]
Hi all,

Actually, I am trying to compute = the dissociation energy of the C1-C2 carbon
bond of = 1,2-diphenylcyclobutane (neutral singlet). I have tried to do so = with
DFT methods, but all of them fail in representing the final = product as an open
shell singlet biradical yielding a closed shell = singlet with <S**2> =3D 0.000
(any atom has spin density on it = and testing the stability of the closed shell
wavefunction against = the open shell one tells me that the closed shell
wavefunction is = stable under the perturbations considered).

Since the = dissociation product is a singlet biradical, I need a =
multideterminantal method such as CASSCF. The problem I have = is the size of
the active space I must consider in my calculations. = If this product would be
a pure biradical, a CASSCF(2,2) would = be enough, but I think that it is more a
biradicaloid, so it needs a = bigger active space. To clutter more this
decision, both = unpaired electrons are on benzylic positions. Therefore, a =
huge CASSCF(14,14) calculation with a proper selection of orbitals = is my
unique option? (the 14 orbitals of the active space come from = the addition of
6 orbitals per phenyl ring plus 2 orbitals of the = benzylic positions).

Thank you in advance,

Jose = Sez

-=3D This is automatically added to each message by = the mailing script =3D-
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With = Best Regards

Tom Albright

= --Apple-Mail-1--395895603-- From owner-chemistry@ccl.net Tue Jul 30 20:41:00 2013 From: "Gerard Pujadas gerard.pujadas(!)gmail.com" To: CCL Subject: CCL: VHELIBS: an easy-to-use open source software for binding site and ligand coordinates validation Message-Id: <-49042-130730190933-3525-oV/HMGKZ5WJ4WuqSfBbeFw||server.ccl.net> X-Original-From: Gerard Pujadas Content-Type: multipart/alternative; boundary=089e014946f41d044004e2c2b32a Date: Wed, 31 Jul 2013 01:09:23 +0200 MIME-Version: 1.0 Sent to CCL by: Gerard Pujadas [gerard.pujadas:_:gmail.com] --089e014946f41d044004e2c2b32a Content-Type: text/plain; charset=ISO-8859-1 Dear CCL list members, first of all, sorry for cross-posting the Nutrigenomics research group (Universitat Rovira i Virgili), the Technological Center for Nutrition and Health and the PDB_REDO developmentteam are proud to announce the *V*alidation *HE*lper for *LI*gands and *B*inding *S*ites (VHELIBS) software. Many Protein Data Bank (PDB ) users assume that the deposited structural models are of high quality but forget that these models are derived from the interpretation of experimental data. The accuracy of atom coordinates is not homogeneous between models or throughout the same model. To avoid basing a research project on a flawed model, we present a tool (i.e., VHELIBS) for assessing the quality of ligands and binding sites in crystallographic models from the PDB. VHELIBS is an open source software that aims to ease the validation of binding site and ligand coordinates for non-crystallographers (i.e., users with little or no crystallography knowledge). Using a convenient graphical user interface, it allows one to check how ligand and binding site coordinates fit to the electron density map. VHELIBScan use models from either the PDB or the PDB_REDO databank of re-refined and re-built crystallographic models. The user can specify threshold values for a series of properties related to the fit of coordinates to electron density (Real Space R, Real Space Correlation Coefficient and average occupancy are used by default). VHELIBSwill automatically classify residues and ligands as Good, Dubious or Bad based on the specified limits. The user is also able to visually check the quality of the fit of residues and ligands to the electron density map and reclassify them if needed. VHELIBSallows inexperienced users to examine the binding site and the ligand coordinates in relation to the experimental data. This is an important step to evaluate models for their fitness for drug discovery purposes such as structure-based pharmacophore development and protein-ligand docking experiments. *Key features of VHELIBS: * - Many different parameters can be used to filter good models, and their threshold values can be adjusted by the user. Contextual help informs the user about the meaning of the different parameters. - VHELIBS comes with three profiles, and the user can create custom profiles and export them for further use or sharing. - VHELIBS has the ability to work with an unlimited number of PDB or UniProtKB codes (all the PDBcodes in each UniProtKB entry are analyzed). - VHELIBS has the ability to choose between models from PDB_REDOor from the PDB . - VHELIBS runs in the Java Virtual Machine, which makes it operating-system independent. - VHELIBS consists of a single jar file, needing no installation. There are no dependencies other than Java. - The user can load a results file from a previous analysis; one can let a huge analysis run during lunch or overnight and then review the results at any later time. - A user does not need to be familiar with any other software (although familiarity with Jmol will help the user to make sophisticated custom views). *There are several cases where VHELIBS can prove very helpful:* - VHELIBS can be used to choose structures to use for a protein-ligand docking: with VHELIBS, the user can choose the structures with the best-modeled binding sites. - VHELIBS can be used to choose structures where both the binding site and the ligand are well modeled, in order to validate the performance of different protein-ligan docking programs. This could make it possible to obtain a new gold standard for protein/ligand complexes that could be used for the validation of docking software and that could be significantly larger and more diverse than those currently being used (i.e., the Astex Diverse Setand the Iridium set ). - VHELIBS can be used to choose structures where both the binding site and the ligand are well modeled to obtain reliable structure-based pharmacophores that select the relevant target bioactivity-modulating intermolecular interactions. This is important in drug-discovery workflows for finding new molecules with similar activity to the co-crystallized ligand. - VHELIBS can be used to obtain well-modeled ligand coordinates in order to evaluate the performance of 3D conformation-generator software that claims to be able to generate bioactive conformations. You can download VHELIBS and read more information about the program by going here . A paper describing VHELIBS has been published at the Journal of Cheminformatics and can be read by going here . Happy validation !!! The VHELIBS team --089e014946f41d044004e2c2b32a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Dear CCL list members,

first of all, = sorry for cross-posting

the Nutrigenomics research group (Universitat Rovira i V= irgili),=A0 the Te= chnological Center for Nutrition and Health and the PDB_REDO developmentteam are= proud to announce the Validation HElper for LIgands a= nd Binding Sites (VHELIBS) software.

Many Protein Data Bank (PDB) users assume that the deposited structural models are of high qu= ality but forget that these models are derived from the interpretation of e= xperimental data. The accuracy of atom coordinates is not homogeneous betwe= en models or throughout the same model. To avoid basing a research project = on a flawed model, we present a tool (i.e., VHELIBS) for assessing = the quality of ligands and binding sites in crystallographic models from th= e PDB.

VHELIBS is an open source software that aims to ease the valida= tion of binding site and ligand coordinates for non-crystallographers (i.e.= , users with little or no crystallography knowledge). Using a convenient gr= aphical user interface, it allows one to check how ligand and binding site = coordinates fit to the electron density map. VHELIBS can use models= from either the PDB o= r the PDB_RED= O databank of re-refined and re-built crystallographic models. The user= can specify threshold values for a series of properties related to the fit= of coordinates to electron density (Real Space R, Real Space Correlation C= oefficient and average occupancy are used by default). VHELIBS will= automatically classify residues and ligands as Good, Dubious or Bad based = on the specified limits. The user is also able to visually check the qualit= y of the fit of residues and ligands to the electron density map and reclas= sify them if needed. VHELIBS allows inexperienced users to examine = the binding site and the ligand coordinates in relation to the experimental= data. This is an important step to evaluate models for their fitness for d= rug discovery purposes such as structure-based pharmacophore development an= d protein-ligand docking experiments.

Key features of VHELIBS:

Many different parame= ters can be used to filter good models, and their threshold values can be a= djusted by the user. Contextual help informs the user about the meaning of = the different parameters.

VHELIBS comes with three profiles, and the user can cr= eate custom profiles and export them for further use or sharing.

VHELIBS has the ability to work with an unlimited number of= PDB or UniProtKB codes (= all the PDB codes in e= ach Uni= ProtKB entry are analyzed).

VHELIBS has the ability to choose between models from = PDB_REDO = or from the PDB.

VHELIBS runs in the Java Virtual Machine, which makes = it operating-system independent.

VHELIBS consists = of a single jar file, needing no installation. There are no dependencies ot= her than Java.

The user can load a results file from a previous analysis; one= can let a huge analysis run during lunch or overnight and then review the = results at any later time.

A user does not need to be fami= liar with any other software (although familiarity with Jmol will help the user to make= sophisticated custom views).

There are several cases where VHELIBS can prove very helpful:=

VHELIBS can be used to choose structures to= use for a protein-ligand docking: with VHELIBS, the user can choos= e the structures with the best-modeled binding sites.

VHELIBS can be used to choose structures where both th= e binding site and the ligand are well modeled, in order to validate the pe= rformance of different protein-ligan docking programs. This could make it p= ossible to obtain a new gold standard for protein/ligand complexes that cou= ld be used for the validation of docking software and that could be signifi= cantly larger and more diverse than those currently being used (i.e., the <= a href=3D"http://www.ncbi.nlm.nih.gov/pubmed/17300160" target=3D"_blank">As= tex Diverse Set and the Iridium set).

VHELIBS can be used to choose structures where both th= e binding site and the ligand are well modeled to obtain reliable structure= -based pharmacophores that select the relevant target bioactivity-modulatin= g intermolecular interactions. This is important in drug-discovery workflow= s for finding new molecules with similar activity to the co-crystallized li= gand.

VHELIBS can be used to obtain well-modeled ligand coor= dinates in order to evaluate the performance of 3D conformation-generator s= oftware that claims to be able to generate bioactive conformations.

You can download VHELIBS and read more information about = the program by going here. A paper describing VHELIBS has b= een published at the Journal of Cheminformatics and can be read by going here.

Happy validation !!!

The VHELIBS team

--089e014946f41d044004e2c2b32a--