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.

Ciao,=

Cina

<= /div>

------------= ---------------------------------------------------------------------

Cina Foroutan-Nej= ad, PhD

Nationa= l Center for Biomolecular Research,

Masaryk University, Brno,

Czech Republic

https://muni.academia.edu/CinaForou= tanNejad

<= br>

On Thursday, 24 July 2014, 23:44, Joe Le= onard jleonard42 : gmail.com <owner-chemistry[A]ccl.net> wrote:

Hmm... How about:

- 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)

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.

Joe

<= div class=3D"" style=3D"">

On Jul 24, 2014, at 3:28 PM, Sebastian Koz= uch seb.kozuch:gmail.com <owner-chemistry{=3D}ccl.net> wrote:

Sent to CCL by: "Sebastian Kozuch" [seb.k= ozuch|a|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 (en.wikipedia.org/wiki/List_of_unsolved_prob= lems), including chemistry.

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,
Sebastian

-=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

E-mail to subscribers: CHEMISTRY{=3D}ccl.n= et or use:
     http://www.ccl.net/cgi-bin/ccl/send_c= cl_message

E-mail to= administrators: CHEMISTRY-REQU= EST{=3D}ccl.net or use
   &nbs= p; http://www.ccl.net/cgi-bi= n/ccl/send_ccl_message

     ht= tp://www.ccl.net/chemistry/sub_unsub.shtml
Before posting, check wait time at: ht= tp://www.ccl.net

Job= : http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.= shtml

If your mail b= ounces > from CCL with 5.7.1 error, check:
&nb= sp;    http://www.ccl.net/spa= mmers.txt

RTFI: http://www.ccl.net/chemistry/abou= tccl/instructions/

=0A

--
How self-centered do you have t= o be to tell yourself that someone else's rights aren't real, but= yours are?

=0A=0A

=0A

---908983334-322261903-1406239871=:51892-- From owner-chemistry@ccl.net Thu Jul 24 20:34:00 2014 From: "Reza Shojaei shojaei81..gmail.com" To: CCL Subject: CCL:G: Restart BOMD calculations Message-Id: <-50355-140724181654-26905-1395kTmPino6/RGYr0lDVg-,-server.ccl.net> X-Original-From: "Reza Shojaei" Date: Thu, 24 Jul 2014 18:16:52 -0400 Sent to CCL by: "Reza Shojaei" [shojaei81^gmail.com] Dear CCL users, I am running BOMD calculations on aniline in order to produce 2000 structures. Due to small allocated memory (3gb) the calculation has stopped at 424th structure. Is there anyway to restart the calculation from check point file with the current input file or I must redo it from the scratch? the Gaussian input file was: %nproc=20 %mem=3000mb %chk=Aniline_bomd_b3lyp_2000_2 # b3lyp aug-cc-pvtz opt Aniline 0 1 C 0.003373 -1.875068 0.000000 C 0.002997 -1.167817 1.197727 C 0.002997 0.219781 1.202958 C 0.002638 0.934969 0.000000 C 0.002997 0.219781 -1.202958 C 0.002997 -1.167817 -1.197727 H 0.003197 -2.955840 0.000000 H 0.002158 -1.699709 2.140109 H 0.007539 0.757751 2.143083 H 0.007539 0.757751 -2.143083 H 0.002158 -1.699709 -2.140109 H -0.273793 2.779860 0.835789 H -0.273793 2.779860 -0.835789 N 0.059571 2.328153 0.000000 --link1-- %nproc=20 %mem=3000Mb %chk=Aniline_bomd_b3lyp_2000_2 # b3lyp aug-cc-pvtz BOMD(MaxPoints=2000,RTemp=298) geom=check IOP(1/44=740613) Aniline 0 1 From owner-chemistry@ccl.net Thu Jul 24 21:09:00 2014 From: "Yelu Shi yshi4]^[stevens.edu" To: CCL Subject: CCL: G09: ONIOM error: Maximum number of microiterations cycles exceeded! Message-Id: <-50356-140724161835-9726-H3lrtIL6rvBZ2QWnm+nUvA[a]server.ccl.net> X-Original-From: "Yelu Shi" Date: Thu, 24 Jul 2014 16:18:33 -0400 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 From owner-chemistry@ccl.net Thu Jul 24 21:44:01 2014 From: "Rajarshi Guha rajarshi.guha__gmail.com" To: CCL Subject: CCL: Call for Papers: Represention, Handling & Modeling of Mixtures and Compound Combinations Message-Id: <-50357-140724174132-9721-FwP/soB0O1X1jLrZz765Yg+/-server.ccl.net> X-Original-From: Rajarshi Guha Content-Type: multipart/alternative; boundary=001a113399744a7b0d04fef75135 Date: Thu, 24 Jul 2014 17:41:21 -0400 MIME-Version: 1.0 Sent to CCL by: Rajarshi Guha [rajarshi.guha-$-gmail.com] --001a113399744a7b0d04fef75135 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear colleagues, we're putting together a thematic issue for J. Cheminf on the topic of mixtures and compound combinations. The issue will consider a wide range of computational issues related to mixtures including representation, storage/handling and modeling of physical properties & biological effects of mixtures and compound combinations. For more details of the intended scope please visit http://www.jcheminf.com/about/update/Mixtures_combination_modeling. If you have any questions regarding topics, submission process or other issues, feel free to contact me at guhar]^[mail.nih.gov. ** Information on publication charge As an open access journal, Journal of Cheminformatics defrays the costs of publishing through article-processing charges because it does not have subscription charges for its content. For this themed issue, we are pleased to provide a 20% discounted publication charge per paper, i.e. =A3936 / EURO 1,128 / $1,568. As well as covering publication charges through their research funds, authors should also check whether:- (1) Their institution has a membership account whereby publication fees are already paid up-front or further discounted (this is rarely known about or used by chemists): please see http://www.chemistrycentral.com/libraries/membership and http://www.chemistrycentral.com/inst/). (2) Their institution/library has institutional funds for supporting open access; this information is most frequently available via the library and their webpages. --=20 Rajarshi Guha | http://blog.rguha.net NIH Center for Advancing Translational Science --001a113399744a7b0d04fef75135 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Dear colleagues, we're putting together a thematic iss= ue for J. Cheminf

on the topic of mixtures and compound combinations. The issue will

con= sider a wide range of computational issues related to mixtures

including representation, storage/handling and modeling of physical

pr= operties & biological effects of mixtures and compound combinations.

= For more details of the intended scope please visit

http://www.jcheminf.com/about/update/Mixtures_combination_modeling.=

If you have any questions regarding topics, submission process or= other

= issues, feel free to contact me at guhar]^[mail.nih.gov.

** Information on publication charge

As an open access journal, Journal of Cheminformatics defrays the costs

of publishing through article-processing charges because it does not

= have subscription charges for its content.

For this themed issue, we are pleased to provide a 20% discounted

publ= ication charge per paper, i.e. =A3936 / €1,128 / $1,568.

As well as covering publication charges through their research fu= nds,

authors should also check whether:-

(1) Their institut= ion has a membership account whereby publication fees

= are already paid up-front or further discounted (this is rarely known

about or used by chemists): please see

http://www.chemistrycen= tral.com/libraries/membership and

= http://= www.chemistrycentral.com/inst/).

(2) Their institution/library

has institutional funds = for supporting open access; this information is

= most frequently available via the library and their webpages.

--
Rajarshi Guha | http://blog.rguha.net
NIH Center for Advancing Translational Science

--001a113399744a7b0d04fef75135-- From owner-chemistry@ccl.net Thu Jul 24 22:19:00 2014 From: "Johannes Johansson johjo76,,gmail.com" To: CCL Subject: CCL: Unsolved Problems Message-Id: <-50358-140724192035-16905-Hwtzp9arFQVv2fPgmL5xAw]![server.ccl.net> X-Original-From: Johannes Johansson Content-Type: multipart/alternative; boundary=089e01494c28d9bf8804fef8b323 Date: Fri, 25 Jul 2014 01:20:29 +0200 MIME-Version: 1.0 Sent to CCL by: Johannes Johansson [johjo76.:.gmail.com] --089e01494c28d9bf8804fef8b323 Content-Type: text/plain; charset=UTF-8 A better understanding of self-interaction in Kohn-Sham DFT, its consequences and how to correct it. This could be one way towards the exact description of XC within KS-DFT. Johannes Den 25 jul 2014 01:12 skrev "Jim Kress jimkress35%%gmail.com" < owner-chemistry-$-ccl.net>: > > Sent to CCL by: "Jim Kress" [jimkress35|gmail.com] > The definition of the exact functionals for exchange and correlation for > use > in DFT as opposed to the plethora of semi-empirical functions being > employed > today. > > Jim > > -----Original Message----- > > From: owner-chemistry+jimkress35==gmail.com#,#ccl.net > [mailto:owner-chemistry+jimkress35==gmail.com#,#ccl.net] On Behalf Of > Sebastian Kozuch seb.kozuch:gmail.com > Sent: Thursday, July 24, 2014 3:28 PM > To: Kress, Jim > Subject: CCL: Unsolved Problems > > > 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, > Sebastianhttp:// > www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > > --089e01494c28d9bf8804fef8b323 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

A better understanding of self-interaction in Kohn-Sham DFT,= its consequences and how to correct it. This could be one way towards the = exact description of XC within KS-DFT.

Johannes

Den 25 jul 2014 01:12 skrev "Jim Kress jimk= ress35%%gmail.com" <owner-chemistry-$-ccl.net>:

Sent to CCL by: "Jim Kress" [jimkress35|gmail.com]
The definition of the exact functionals for exchange and correlation for us= e
in DFT as opposed to the plethora of semi-empirical functions being employe= d
today.

Jim

-----Original Message-----
> From: owner-chemistry+jimkress35=3D=3Dgmail.com#,#ccl.net
[mailto:owner-chemistry+jim= kress35=3D=3Dg= mail.com#,#ccl.net] On Behalf Of
Sebastian Kozuch seb.kozuch:= gmail.com
Sent: Thursday, July 24, 2014 3:28 PM
To: Kress, Jim
Subject: CCL: Unsolved Problems

Sent to CCL by: "Sebastian =C2=A0Kozuch" [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 unsolve= d
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<= br> Chemistry?

(Please dont say something obvious like solving the relativistic full CI of=
a protein.)

Best,
Sebastianhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.n= et/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY-$-ccl.n= et or use:
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message=

E-mail to administrators: CHEM= ISTRY-REQUEST-$-ccl.net or use
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message=

Subscribe/Unsubscribe:
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Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/

--089e01494c28d9bf8804fef8b323-- From owner-chemistry@ccl.net Thu Jul 24 22:54:00 2014 From: "Brian Skinn bskinn%alum.mit.edu" To: CCL Subject: CCL: Unsolved Problems Message-Id: <-50359-140724192346-19507-NMxiVRLpZY/HlHUeri0fdw^^^server.ccl.net> X-Original-From: Brian Skinn Content-Type: multipart/alternative; boundary=047d7b450a7c375a8504fef8bfe7 Date: Thu, 24 Jul 2014 19:23:20 -0400 MIME-Version: 1.0 Sent to CCL by: Brian Skinn [bskinn^alum.mit.edu] --047d7b450a7c375a8504fef8bfe7 Content-Type: text/plain; charset=UTF-8 Functionals that address directly the defect associated with calculating the electron kinetic energy using non-interacting orbitals. -Brian On Thu, Jul 24, 2014 at 5:38 PM, Rajarshi Guha guhar]=[mail.nih.gov < owner-chemistry[]ccl.net> wrote: > One more for the list - a statistical basis for structural similarity > (something akin to BLAST e-values that is not dependent on a specific > sample of structures) > > > On Thu, Jul 24, 2014 at 4:25 PM, Joe Leonard jleonard42 : gmail.com < > owner-chemistry|ccl.net> wrote: > >> 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 < >> owner-chemistry{}ccl.net> 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>> the strange characters on the top line to the {} sign. You can also >> E-mail to subscribers: CHEMISTRY{}ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST{}ccl.net or use>> >> If your mail bounces > from CCL with 5.7.1 error, check:>> >> >> >> -- >> How self-centered do you have to be to tell yourself that someone else's >> rights aren't real, but yours are? >> >> >> >> > > > -- > Rajarshi Guha | http://blog.rguha.net > National Center for Advancing Translational Science > --047d7b450a7c375a8504fef8bfe7 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Functionals that address directly the defect associated wi= th calculating the electron kinetic energy using non-interacting orbitals.<= div>

-Brian

On Thu, Jul 24, 2014 at 5:38 PM, Rajarshi Guha guhar]=3D[mail.nih.gov <owner-chemistry[]ccl.net> wrote:

One more for the list - a s= tatistical basis for structural similarity (something akin to BLAST e-value= s that is not dependent on a specific sample of structures)

On Thu, Jul 24, 2014 at 4:25 PM, Joe Leonard jleonard42 : gmail.com <owner-chemistry|ccl= .net> wrote:

Hmm... =C2=A0How about:

- A (docking) scor= ing function that actually worked - was predictive, extensible and reproduc= ible

- A force field that worked well for both large and small molecules (s= eparately and in combination)

Are these on the lev= el of string theory? =C2=A0No. =C2=A0But there's real, concrete problem= s facing industrial (and some academic) researchers that should be addresse= d. =C2=A0There are others, but this should get things started.

Joe

On Ju= l 24, 2014, at 3:28 PM, Sebastian Kozuch seb.kozuch:gmail.com <owner-chemistry{}ccl.net> wrote:

Sent to CCL by: &qu= ot;Sebastian =C2=A0Kozuch" [seb.kozuch|a|gmail.com]
Dear CCL users,
Except for some bash= ing to a particular computational chemistry journal, in the last months we = have been slow on controversial and/or philosophical questions (it feels li= ke the double blind reviewing and the patriarchalization of conferences deb= ates happened ages ago).
So here is a question. It draw my attention that there are lists of unsolve= d problems on several topics (en.wikipedia.org/wiki/List_of_unsol= ved_problems), including chemistry.

What would be a List of Unsolved Problems in Theoretical and Computatio= nal Chemistry?

(Please dont say something obvious like solving the r= elativistic full CI of a protein.)

Best,
Sebastian

-=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
E-mail to subscribers: CHEMISTRY{}ccl.net or use:
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST{}ccl.net or us= e
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0http://www.ccl.net/cgi-bin/ccl/send_= ccl_message

=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0http://www.ccl.= net/chemistry/sub_unsub.shtml

Before posting, check wait time at= : http://www.ccl.net
Job: http://www.c= cl.net/jobs
Conferences: http://server.ccl.net/chemis= try/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.sht= ml

If your mail bounces > from CCL with 5.7.1 error, check: =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0http://www.ccl.net/spammers.txt

RTFI: = http://www.ccl.net/chemistry/aboutccl/instructions/

--
How se= lf-centered do you have to be to=C2=A0tell yourself that someone=C2=A0else&= #39;s rights aren't real, but yours are?

--
R= ajarshi Guha |=C2=A0ht= tp://blog.rguha.net
National Center for Advancing Translational Science

--047d7b450a7c375a8504fef8bfe7-- From owner-chemistry@ccl.net Thu Jul 24 23:29:00 2014 From: "Joe Leonard jleonard42-.-gmail.com" To: CCL Subject: CCL: Unsolved Problems Message-Id: <-50360-140724205721-18995-txlF73cj5SwvjLAMwF/y7w:server.ccl.net> X-Original-From: Joe Leonard Content-Type: multipart/alternative; boundary="Apple-Mail=_BF7586D8-D143-4613-88F0-C3760686E8CC" Date: Thu, 24 Jul 2014 20:57:12 -0400 Mime-Version: 1.0 (Mac OS X Mail 7.3 $1878.6$) Sent to CCL by: Joe Leonard [jleonard42+*+gmail.com] --Apple-Mail=_BF7586D8-D143-4613-88F0-C3760686E8CC Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Thought of two more: - a pka model or method good / fast enough to indicate which atoms = should or shouldn't be protonated at biological ph. Extra points if = this can be used iteratively when multiple centres are present. This = should work with drug like molecules and be extensible to peptides and = proteins.=20 This of course should work generally rather than being training set = dependent etc.=20 - "a qm-based pharmacophore scheme". A model for Hbond prediction and = proton donor / acceptor that's not rule based.=20 Joe On Jul 24, 2014, at 5:38 PM, Rajarshi Guha guhar]=3D[mail.nih.gov = wrote: > One more for the list - a statistical basis for structural similarity = (something akin to BLAST e-values that is not dependent on a specific = sample of structures) >=20 >=20 > On Thu, Jul 24, 2014 at 4:25 PM, Joe Leonard jleonard42 : gmail.com = wrote: > Hmm... How about: >=20 > - 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) >=20 > 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. >=20 > Joe >=20 > On Jul 24, 2014, at 3:28 PM, Sebastian Kozuch seb.kozuch:gmail.com = wrote: >=20 >>=20 >> 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.=20= >>=20 >> What would be a List of Unsolved Problems in Theoretical and = Computational Chemistry? >>=20 >> (Please dont say something obvious like solving the relativistic full = CI of a protein.) >>=20 >> Best, >> Sebastian >>=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 >> the strange characters on the top line to the {} sign. You can also >>=20 >>=20 >> E-mail to subscribers: CHEMISTRY{}ccl.net or use:>>=20 >> E-mail to administrators: CHEMISTRY-REQUEST{}ccl.net or use>>=20>>=20 >> Job: http://www.ccl.net/jobs=20 >> Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >>=20>>=20 >> If your mail bounces > from CCL with 5.7.1 error, check:>>=20>>=20 >>=20 >=20 > -- > How self-centered do you have to be to tell yourself that someone = else's rights aren't real, but yours are? >=20 >=20 >=20 >=20 >=20 >=20 > --=20 > Rajarshi Guha | http://blog.rguha.net > National Center for Advancing Translational Science -- How self-centered do you have to be to tell yourself that someone else's = rights aren't real, but yours are? --Apple-Mail=_BF7586D8-D143-4613-88F0-C3760686E8CC Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=iso-8859-1 Thought of two more:

- a pka = model or method good / fast enough to indicate which atoms should or = shouldn't be protonated at biological ph. Extra points if this can = be used iteratively when multiple centres are present. This should = work with drug like molecules and be extensible to peptides and = proteins.

This of course should work = generally rather than being training set dependent = etc.

- "a qm-based pharmacophore scheme". = A model for Hbond prediction and proton donor / acceptor that's not rule = based.

Joe

On Jul 24, = 2014, at 5:38 PM, Rajarshi Guha guhar]=3D[mail.nih.gov <owner-chemistry(0)ccl.net> = wrote:

One more for the list - a statistical = basis for structural similarity (something akin to BLAST e-values that = is not dependent on a specific sample of structures)

On Thu, Jul 24, 2014 at 4:25 PM, Joe Leonard jleonard42 : gmail.com <owner-chemistry|ccl.net> wrote:

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 <owner-chemistry{}ccl.net> 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

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National Center for = Advancing Translational Science

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