From owner-chemistry@ccl.net Fri Jul 25 03:42:02 2014 From: "Michel Petitjean petitjean.chiral-x-gmail.com" To: CCL Subject: CCL: Unsolved Problems Message-Id: <-50361-140725034016-22712-pV/M2LmPjW+uUIdnFgtE5Q*_*server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Fri, 25 Jul 2014 09:40:05 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral-*-gmail.com] The following problems may be considered as mathematical ones, but they could be of interest for the computational chemist. Chirality (any measure you like): * Find the maximally (possibly asymptotic) chiral distribution of points in R^3 (discrete or continuous; no graph, no labeling). * Find the maximally chiral tetrahedron (non labeled set of 4 points). Remark: before defining your own chirality measure, please check that it makes sense at least in the simplest situations (e.g. unidimensional finite sets) Geometric docking (no charge): * Define a scale independant index taking values in [0..1] measuring the degree of geometric docking * Once defined, find non trivial shapes realizing the maximum of the index, then the minimum of the index Remark: the bidimensional case is of interest, too. Michel Petitjean MTi, INSERM UMR-S 973, University Paris 7, 35 rue Helene Brion, 75205 Paris Cedex 13, France. Phone: +331 5727 8434; Fax: +331 5727 8372 E-mail: petitjean.chiral|gmail.com (preferred), michel.petitjean|univ-paris-diderot.fr http://petitjeanmichel.free.fr/itoweb.petitjean.html http://petitjeanmichel.free.fr/itoweb.petitjean.shape.html 2014-07-24 22:25 GMT+02:00 Joe Leonard jleonard42 : gmail.com : > Hmm... How about: > > - A (docking) scoring function that actually worked - was predictive, extensible and reproducible > - A force field that worked well for both large and small molecules (separately and in combination) > > Are these on the level of string theory? No. But there's real, concrete problems facing industrial (and some academic) researchers that should be addressed. There are others, but this should get things started. > > Joe > > On Jul 24, 2014, at 3:28 PM, Sebastian Kozuch seb.kozuch:gmail.com > wrote: > > > Sent to CCL by: "Sebastian Kozuch" [seb.kozuch|a|gmail.com] > Dear CCL users, > Except for some bashing to a particular computational chemistry journal, in the last months we have been slow on controversial and/or philosophical questions (it feels like the double blind reviewing and the patriarchalization of conferences debates happened ages ago). > So here is a question. It draw my attention that there are lists of unsolved problems on several topics > (en.wikipedia.org/wiki/List_of_unsolved_problems), including chemistry. > > What would be a List of Unsolved Problems in Theoretical and Computational Chemistry? > > (Please dont say something obvious like solving the relativistic full CI of a protein.) > > Best, > Sebastian > From owner-chemistry@ccl.net Fri Jul 25 04:24:00 2014 From: "Demetra Dimetrodon dpfiz[*]hotmail.com" To: CCL Subject: CCL: Unsolved Problems Message-Id: <-50362-140725042040-21348-kBcj5DeJaf8KcqDlvBZjuQ*_*server.ccl.net> X-Original-From: "Demetra Dimetrodon" Date: Fri, 25 Jul 2014 04:20:38 -0400 Sent to CCL by: "Demetra Dimetrodon" [dpfiz^^hotmail.com] Totally true. For example, the LCAO approximation. What is the mechanism for spins flipping upon the formation of a covalent bond, for example in O_2 formation? > "Cina Foroutan-Nejad canyslopus^^^yahoo.co.uk" wrote: > > Sent to CCL by: Cina Foroutan-Nejad [canyslopus ~ yahoo.co.uk] > ---908983334-322261903-1406239871=:51892 > Content-Type: text/plain; charset=iso-8859-1 > Content-Transfer-Encoding: quoted-printable > > The biggest unsolved problem of computational chemistry is "chemical bond".= > If one looks at the list of bond theories will realize how critical it is.= > So many debates and finally nothing acceptable for all. This is in fact a = > part of a deeper question: "is chemistry reducible to physics?". How to def= > ine chemical concepts in the context of physics. Chemical bond, aromaticity= > , alpha effect, etc. It looks so old-fashioned but I think it looks old-fas= > hioned because people are tired of endless discussions.=0A=0ACiao,=0ACina= > =0A=0A---------------------------------------------------------------------= > ------------=0ACina Foroutan-Nejad, PhD=0ANational Center for Biomolecular = > Research,=0AMasaryk University, Brno,=0ACzech Republic=0Ahttps://muni.acade= > mia.edu/CinaForoutanNejad=0A=0A=0A=0AOn Thursday, 24 July 2014, 23:44, Joe = > Leonard jleonard42 : gmail.com wrote:=0A =0A=0A= > =0AHmm... =A0How about:=0A=0A- A (docking) scoring function that actually w= > orked - was predictive, extensible and reproducible=0A- A force field that = > worked well for both large and small molecules (separately and in combinati= > on)=0A=0AAre these on the level of string theory? =A0No. =A0But there's rea= > l, concrete problems facing industrial (and some academic) researchers that= > should be addressed. =A0There are others, but this should get things start= > ed.=0A=0AJoe=0A=0A=0AOn Jul 24, 2014, at 3:28 PM, Sebastian Kozuch seb.kozu= > ch:gmail.com wrote:=0A=0A=0A>Sent to CCL by: = > "Sebastian =A0Kozuch" [seb.kozuch|a|gmail.com]=0A>Dear CCL users,=0A>Except= > for some bashing to a particular computational chemistry journal, in the l= > ast months we have been slow on controversial and/or philosophical question= > s (it feels like the double blind reviewing and the patriarchalization of c= > onferences debates happened ages ago).=0A>So here is a question. It draw my= > attention that there are lists of unsolved problems on several topics (en.= > wikipedia.org/wiki/List_of_unsolved_problems), including chemistry. =0A>=0A= > >What would be a List of Unsolved Problems in Theoretical and Computational= > Chemistry?=0A>=0A>(Please dont say something obvious like solving the rela= > tivistic full CI of a protein.)=0A>=0A>Best,=0A>Sebastian=0A>=0A>=0A>=0A>-= > =3D This is automatically added to each message by the mailing script =3D-= > =0A>To recover the email address of the author of the message, please chang= > e=0A>the strange characters on the top line to the {=3D} sign. You can also= > =0A=0A>=0A>E-mail to = > subscribers: CHEMISTRY{=3D}ccl.net or use:=0A>=A0=A0=A0=A0=A0http://www.ccl= > .net/cgi-bin/ccl/send_ccl_message=0A>=0A>E-mail to administrators: CHEMISTR= > Y-REQUEST{=3D}ccl.net or use=0A>=A0=A0=A0=A0=A0http://www.ccl.net/cgi-bin/c= > cl/send_ccl_message=0A>=0A>=A0=A0=A0=A0=A0http://www.ccl.net/chemistry/sub_= > unsub.shtml=0A>=0A= > =0A>=0A=0A>Conferences: http://server.ccl.net= > /chemistry/announcements/conferences/=0A>=0A>Search Messages: http://www.cc= > l.net/chemistry/searchccl/index.shtml=0A>=0A>If your mail bounces > from CC= > L with 5.7.1 error, check:=0A>=A0=A0=A0=A0=A0http://www.ccl.net/spammers.tx= > t=0A>=0A=0A>=0A>= > =0A>=0A=0A--=0AHow self-centered do you have to be to=A0tell yourself that = > someone=A0else's rights aren't real, but yours are? > ---908983334-322261903-1406239871=:51892 > Content-Type: text/html; charset=iso-8859-1 > Content-Transfer-Encoding: quoted-printable > >
lveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, Sans-Serif;fo= > nt-size:10pt">
The biggest unsolved problem of co= > mputational chemistry is "chemical bond". If one looks at the list of bond = > theories will realize how critical it is. So many debates and finally nothi= > ng acceptable for all. This is in fact a part of a deeper question: "is che= > mistry reducible to physics?". How to define chemical concepts in the conte= > xt of physics. Chemical bond, aromaticity, alpha effect, etc. It looks so o= > ld-fashioned but I think it looks old-fashioned because people are tired of= > endless discussions.

=3D"">
: HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-= > serif; font-style: normal; background-color: transparent;" class=3D"">Ciao,= >
style=3D"color: rgb(0, 0, 0); font-size: 13px; font-family: HelveticaNeue,= > 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; font-styl= > e: normal; background-color: transparent;" class=3D"">Cina
=3D"color: rgb(0, 0, 0); font-size: 13px; font-family: HelveticaNeue, 'Helv= > etica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; font-style: nor= > mal; background-color: transparent;" class=3D"">
<= > /div>
ticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; = > font-style: normal; background-color: transparent;" class=3D"">------------= > ---------------------------------------------------------------------
= >
eue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-serif; font-= > style: normal; background-color: transparent;" class=3D"">Cina Foroutan-Nej= > ad, > PhD
HelveticaNeue, 'Helvetica Neue', Helvetica, Arial, 'Lucida Grande', sans-se= > rif; font-style: normal; background-color: transparent;" class=3D"">Nationa= > l Center for Biomolecular Research,
font-size: 13px; font-family: HelveticaNeue, 'Helvetica Neue', Helvetica, = > Arial, 'Lucida Grande', sans-serif; font-style: normal; background-color: t= > ransparent;" class=3D"">Masaryk University, Brno,
rgb(0, 0, 0); font-size: 13px; font-family: HelveticaNeue, 'Helvetica Neue= > ', Helvetica, Arial, 'Lucida Grande', sans-serif; font-style: normal; backg= > round-color: transparent;" class=3D"">Czech Republic
kground-color: transparent;" class=3D"">https://muni.academia.edu/CinaForou= > tanNejad

<= > br>
=3D"font-family: > HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, Sans-Serif= > ; font-size: 10pt;" class=3D"">
elvetica Neue, Helvetica, Arial, Lucida Grande, Sans-Serif; font-size: 12pt= > ;" class=3D"">
e=3D"Arial" class=3D"" style=3D""> On Thursday, 24 July 2014, 23:44, Joe Le= > onard jleonard42 : gmail.com <owner-chemistry[A]ccl.net> wrote:
s=3D"" style=3D"">


style=3D"">
" style=3D"">
Hmm...  How about:
=3D"" style=3D"">
>- A (docking) scoring function that actually worked - was predictive, exte= > nsible and reproducible
- A force field tha= > t worked well for both large and small molecules (separately and in combina= > tion)

style=3D"">
Are these on the level of stri= > ng theory?  No.  But there's real, concrete problems facing indus= > trial (and some academic) researchers that should be addressed.  There= > are others, but this should get things started.
=3D"">
Joe
<= > div class=3D"" style=3D"">
=3D"">
On Jul 24, 2014, at 3:28 PM, Sebastian Koz= > uch seb.kozuch:gmail.com < emistry{=3D}ccl.net" target=3D"_blank" href=3D"mailto:owner-chemistry{=3D}c= > cl.net" class=3D"" style=3D"">owner-chemistry{=3D}ccl.net> wrote: iv>
">
Sent to CCL by: "Sebastian  Kozuch" [seb.k= > ozuch|a| ass=3D"" style=3D"">gmail.com]
Dear CCL > users,
Except for some bashing to a particular co= > mputational chemistry journal, in the last months we have been slow on cont= > roversial and/or philosophical questions (it feels like the double blind re= > viewing and the patriarchalization of conferences debates happened ages ago= > ).
So here is a question. It draw my attention tha= > t there are lists of unsolved problems on several topics ( w" target=3D"_blank" href=3D"http://en.wikipedia.org/wiki/List_of_unsolved_= > problems" class=3D"" style=3D"">en.wikipedia.org/wiki/List_of_unsolved_prob= > lems), including chemistry.

yle=3D"">What would be a List of Unsolved Problems in Theoretical and Compu= > tational Chemistry?

(Ple= > ase dont say something obvious like solving the relativistic full CI of a p= > rotein.)

Best,
=3D"" style=3D"">Sebastian
style=3D"">


=3D"" style=3D"">-=3D This is automatically added to each message by the ma= > iling script =3D-
To recover the email address of = > the author of the message, please change
the stran= > ge characters on the top line to the {=3D} sign. You can also
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   &nbs= > p;  i-bin/ccl/send_ccl_message" class=3D"" style=3D"">http://www.ccl.net/cgi-bi= > n/ccl/send_ccl_message

"">       f=3D"http://www.ccl.net/chemistry/sub_unsub.shtml" class=3D"" style=3D"">ht= > tp://www.ccl.net/chemistry/sub_unsub.shtml
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style=3D"">

le=3D"">
=0A
ap:break-word;" class=3D"">
rd;" class=3D"">--
How self-centered do you have t= > o be to tell yourself that someone else's rights aren't real, but= > yours are?


"" style=3D"">
=0A=0A
=0A
div>


>
> ---908983334-322261903-1406239871=:51892-- > > From owner-chemistry@ccl.net Fri Jul 25 07:09:00 2014 From: "Hanna Thamleena hannathamleena#gmail.com" To: CCL Subject: CCL: G09: ONIOM error: Maximum number of microiterations cycles exceeded! Message-Id: <-50363-140725021009-26864-DcLZ7yM/kzDFN/rwjvF1hw-,-server.ccl.net> X-Original-From: Hanna Thamleena Content-Type: multipart/alternative; boundary=089e01184b0c8ea7c904fefe6cbc Date: Fri, 25 Jul 2014 11:40:03 +0530 MIME-Version: 1.0 Sent to CCL by: Hanna Thamleena [hannathamleena+/-gmail.com] --089e01184b0c8ea7c904fefe6cbc Content-Type: text/plain; charset=UTF-8 Hi Yelu You can switch off the microiterations by opt=nomicro keyword. Hanna Thamleena Research Scholar National institute of Technology Calicut INDIA On Fri, Jul 25, 2014 at 1:48 AM, Yelu Shi yshi4]^[stevens.edu < owner-chemistry::ccl.net> wrote: > > Sent to CCL by: "Yelu Shi" [yshi4---stevens.edu] > I would like to perform an ONIOM (QM/MM)optimization with electronic > embedding. > I finished an ONIOM (QM/MM) optimization without electronic embedding > first. > Then with the optimized sturcture, I performed the ONIOM optimization with > electronic embedding. When the optimization ran the first step, there was > an > error message: Maximum number of microiterations cycles exceeded! And the > job > was terminated. My route section is: # opt=maxcycles=512 > oniom(mpwvwn/gen:amber=hardfirst)=embedcharge nosymm > geom=connectivity scf=(fermi,xqc) > > How can I fix this error and let the optimization running? > > Thanks a lot. > Yelu> > > --089e01184b0c8ea7c904fefe6cbc Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi Yelu

You can switch off the microite= rations by opt=3Dnomicro keyword.=C2=A0

Hanna Thamleena
Research Sch= olar
National institute of Technology Calicut
INDIA


On Fri, Jul 25, 2014 at 1:48 AM, Yelu Sh= i yshi4]^[stevens.edu = <owner-chem= istry::ccl.net> wrote:

Sent to CCL by: "Yelu =C2=A0Shi" [yshi4---stevens.edu]
I would like to perform an ONIOM (QM/MM)optimization with electronic embedd= ing.
I finished an ONIOM (QM/MM) optimization without electronic embedding first= .
Then with the optimized sturcture, I performed the ONIOM optimization with<= br> electronic embedding. When the optimization ran the first step, there was a= n
error message: Maximum number of microiterations cycles exceeded! And the j= ob
was terminated. My route section is: # opt=3Dmaxcycles=3D512
oniom(mpwvwn/gen:amber=3Dhardfirst)=3Dembedcharge nosymm
geom=3Dconnectivity scf=3D(fermi,xqc)

How can I fix this error and let the optimization running?

Thanks a lot.
Yelu



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--089e01184b0c8ea7c904fefe6cbc-- From owner-chemistry@ccl.net Fri Jul 25 07:44:00 2014 From: "Vladimir Chupakhin chupvl() gmail.com" To: CCL Subject: CCL: Attention Scientists: Register for the Tox21 Data Challenge 2014 Message-Id: <-50364-140725033411-22018-pV/M2LmPjW+uUIdnFgtE5Q[]server.ccl.net> X-Original-From: Vladimir Chupakhin Content-Type: multipart/alternative; boundary=001a11397660f2070104feff98c5 Date: Fri, 25 Jul 2014 09:33:22 +0200 MIME-Version: 1.0 Sent to CCL by: Vladimir Chupakhin [chupvl a gmail.com] --001a11397660f2070104feff98c5 Content-Type: text/plain; charset=UTF-8 Hello Ruili, nice initiative, but when the data will be available? Best regards! Vladimir Chupakhin On Thu, Jul 24, 2014 at 8:18 PM, Ruili Huang huangru]~[mail.nih.gov < owner-chemistry[#]ccl.net> wrote: > > Sent to CCL by: "Ruili Huang" [huangru[#]mail.nih.gov] > NCATS Launches Chemical Toxicity Data Model Competition > > The National Center for Advancing Translational Sciences (NCATS) announces > the Toxicology in the 21st Century (Tox21) Data Challenge 2014 competition. > > The goal of the challenge is to crowdsource data analysis by independent > researchers in order to develop computational models that can better > predict chemical toxicity. It is designed to improve current toxicity > assessment methods, which are often slow and costly. The model submission > deadline is Nov. 14, 2014, 11:59 p.m. ET. NCATS will showcase the winning > models in January 2015. > > Registration for the challenge and more information can be found at > https://tripod.nih.gov/tox21/challenge/. > > Tox21 scientists are currently testing a library of more than 10,000 > chemical compounds in NCATSs high-throughput robotic screening system. To > date, the team has produced nearly 50 million data points from screening > the chemical library against cell-based assays. Data generated from twelve > of these assays form the basis of the 2014 challenge. > > For more information on the Tox21 Modeling Challenge and Tox21 Program > contact: > > Anna Rossoshek > rossosheka-$-mail.nih.gov > > 9800 Medical Center Drive > Rockville, MD 20850 USA> > > --001a11397660f2070104feff98c5 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hello Ruili,

nice initiative, but when = the data will be available?

Best regards!

Vladimir Chupakhin


On Thu, Jul 24, 2014 at 8:18 PM, Ruili Huang= huangru]~[mail.nih.gov <owner-c= hemistry[#]ccl.net> wrote:

Sent to CCL by: "Ruili =C2=A0Huang" [huangru[#]mail.nih.gov]
NCATS Launches Chemical Toxicity Data Model Competition

The National Center for Advancing Translational Sciences (NCATS) announces = the Toxicology in the 21st Century (Tox21) Data Challenge 2014 competition.=

The goal of the challenge is to crowdsource data analysis by independent re= searchers in order to develop computational models that can better predict = chemical toxicity. It is designed to improve current toxicity assessment me= thods, which are often slow and costly. The model submission deadline is No= v. 14, 2014, 11:59 p.m. ET. NCATS will showcase the winning models in Janua= ry 2015.

Registration for the challenge and more information can be found at https://trip= od.nih.gov/tox21/challenge/.

Tox21 scientists are currently testing a library of more than 10,000 chemic= al compounds in NCATSs high-throughput robotic screening system. To date, t= he team has produced nearly 50 million data points from screening the chemi= cal library against cell-based assays. Data generated from twelve of these = assays form the basis of the 2014 challenge.

For more information on the Tox21 Modeling Challenge and Tox21 Program cont= act:

Anna Rossoshek
rossosheka-$-mail.nih.gov=

9800 Medical Center Drive
Rockville, MD 20850 USA



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--001a11397660f2070104feff98c5-- From owner-chemistry@ccl.net Fri Jul 25 09:40:00 2014 From: "Ruili Huang huangru!=!mail.nih.gov" To: CCL Subject: CCL: Attention Scientists: Register for the Tox21 Data Challenge 2014 Message-Id: <-50365-140725093813-6883-nq+HtoafNJs8COnwPoHZuA~~server.ccl.net> X-Original-From: "Ruili Huang" Date: Fri, 25 Jul 2014 09:38:12 -0400 Sent to CCL by: "Ruili Huang" [huangru ~ mail.nih.gov] Hi Vladimir, The data is available from the challenge website. Youll be able to download the data once you register for the challenge. Best, Ruili