From owner-chemistry@ccl.net Tue Feb 25 04:17:00 2014 From: "Mark Andrew Blitz m.blitz%a%leeds.ac.uk" To: CCL Subject: CCL: Mesmer 3.0 Message-Id: <-49800-140225041513-24521-zqPgfuMhpMuKJf8sZD/mkA]-[server.ccl.net> X-Original-From: "Mark Andrew Blitz" Date: Tue, 25 Feb 2014 04:15:12 -0500 Sent to CCL by: "Mark Andrew Blitz" [m.blitz\a/leeds.ac.uk] Dear Colleagues, On behalf of the MESMER team, I am delighted to announce that MESMER 3.0 (Master Equation Solver for Multi Energy-well Reactions) is now available for download. The Windows installer and Linux tar file are located at: http://sourceforge.net/projects/mesmer/ The source can also be viewed and downloaded from this site. There are also bug and feature request tracking facilities which we encourage you to use. The following new features have been incorporated: Extension of experimental specification to include bath gas. The ability to analyse Hessian matrices to exclude internal rotor modes prior to the determination of vibrational frequencies. Addition of a new reaction type pseudo isomerization. Analytical representation of rate coefficients using Chebyshev polynomials in Cantera and Chemkin formats. XML Schema support to assist with input file specification. If you have any comments or suggestions, please dont hesitate to let us know, either through the above site or by email (Mark Blitz (M.Blitz_+_leeds.ac.uk), Robin Shannon(r.shannon_+_leeds.ac.uk) and Struan Robertson (Struanhrobertson_+_gmail.com) would be very happy to receive feedback). We have recently published an article that describes some of the implementation details of MESMER (Journal of Physical Chemistry A, 95459560, 116 (2012)). More information is available at the MESMER website: http://www.chem.leeds.ac.uk/mesmer.html The MESMER team also participate in the MEIC (Master Equation Inter- Comparison), details of which are available from Prof. John Barker (jrbarker_+_umich.edu). With best regards, Mark Blitz From owner-chemistry@ccl.net Tue Feb 25 04:52:00 2014 From: "=?iso-8859-2?Q?=22Marcin_Kr=F3l=22?= mykrol .. cyf-kr.edu.pl" To: CCL Subject: CCL: Energy conformers for ligands in bund protein structures Message-Id: <-49801-140225041347-24212-l/GvznfEo2jKzjpeqd4OjQ ~~ server.ccl.net> X-Original-From: =?iso-8859-2?Q?=22Marcin_Kr=F3l=22?= Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-2 Date: Tue, 25 Feb 2014 10:13:37 +0100 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-2?Q?=22Marcin_Kr=F3l=22?= [mykrol a cyf-kr.edu.pl] Hi Katy You need to run two calculations, one would be just to estimate energy of the bioactive conformation of your ligand taken from the protein and the other would be to run a geometry optimization of the ligand and compare the energies of bioactive and minimized conformations. Depending on the level of theory you want to apply you can start with Macromodel, go to Macromodel/CurrentEnergy to get the estimate of energy for the bioactive conformation (if you want in vacuum choose the correct solvent option) and for the second calculation go to Macromodel/Minimization (or Macromodel/Conformational Search + Minimization if you compound has a rough energy surface). Bear in mind energy difference is on the force-field level. Prior to Macromodel calculations you need to add hydrogens to your ligand with Ligprep. Then, if you want QM level of theory you can use Jaguar and again run single point and optimization calculations and compare the final energies. Best marcin > > Sent to CCL by: "kathryn emily kellett" [k.kellett]=[herts.ac.uk] > I am trying to find a way of comparing the energy of my ligand in my > protein from the PDB with a minimum energy conformation in vacuo. Does > anyone know any way of doing this using either Maestro (for which I have a > licence) or using freely accessible software. > > I want to make sure I am comparing like with like, ie both in vacuo rather > then orientation in crysal structure with solvation energies taken into > account. > > thanks, > > Katy k.kellett|a|herts.ac.uk> > > From owner-chemistry@ccl.net Tue Feb 25 08:53:00 2014 From: "Billy McCann thebillywayne^gmail.com" To: CCL Subject: CCL: Mesmer 3.0 Message-Id: <-49802-140225085114-32368-bGPL7hcygXq72fXhx+mVww!^!server.ccl.net> X-Original-From: Billy McCann Content-Type: multipart/alternative; boundary=001a11c214de3ea6b004f33b6110 Date: Tue, 25 Feb 2014 08:50:51 -0500 MIME-Version: 1.0 Sent to CCL by: Billy McCann [thebillywayne#gmail.com] --001a11c214de3ea6b004f33b6110 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable There's a tiny typo in the reference (no hyphen in the page range). J. Phys. Chem. A, 2012, 116 (38), pp 9545=E2=80=939560 DOI*: *10.1021/jp3051033 ------------------------------------------[00(01|10)11] ----------------------------------------- Billy Wayne McCann, Ph.D. Google+ PGP Key irc://irc.freenode.net:bwayne MzM0LTcwMy0wMTIyCg=3D=3D | base64 "A rich man will always desire what his wealth cannot acquire." ~ Faust (Goethe) ------------------------------------------[11(10|01)00]------- ----------------------------------- On Tue, Feb 25, 2014 at 4:15 AM, Mark Andrew Blitz m.blitz%a%leeds.ac.uk < owner-chemistry:ccl.net> wrote: > > Sent to CCL by: "Mark Andrew Blitz" [m.blitz\a/leeds.ac.uk] > Dear Colleagues, > > On behalf of the MESMER team, I am delighted to announce that MESMER 3.0 > (Master Equation Solver for Multi Energy-well Reactions) is now available > for > download. > > The Windows installer and Linux tar file are located at: > > http://sourceforge.net/projects/mesmer/ > > The source can also be viewed and downloaded from this site. There are al= so > bug and feature request tracking facilities which we encourage you to use= . > > The following new features have been incorporated: > Extension of experimental specification to include bath gas. > The ability to analyse Hessian matrices to exclude internal rotor modes > prior to the determination of vibrational frequencies. > Addition of a new reaction type pseudo isomerization. > Analytical representation of rate coefficients using Chebyshev polynomia= ls > in Cantera and Chemkin formats. > XML Schema support to assist with input file specification. > > If you have any comments or suggestions, please dont hesitate to let us > know, either through the above site or by email (Mark Blitz > (M.Blitz/a\leeds.ac.uk), Robin Shannon(r.shannon/a\leeds.ac.uk) and Strua= n > Robertson (Struanhrobertson/a\gmail.com) would be very happy to receive > feedback). > > We have recently published an article that describes some of the > implementation details of MESMER (Journal of Physical Chemistry A, > 95459560, > 116 (2012)). > > More information is available at the MESMER website: > http://www.chem.leeds.ac.uk/mesmer.html > > The MESMER team also participate in the MEIC (Master Equation Inter- > Comparison), details of which are available from Prof. John Barker > (jrbarker/a\umich.edu). > > > With best regards, > > Mark Blitz > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --001a11c214de3ea6b004f33b6110 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
There's a tiny typo in the reference (no hyphen in the page rang= e).
J. Phys. Chem. A, 2012, 116 (38), pp 9545=E2=80=939560
DOI: 10.1021/jp3051033


<= div>-----------------------------= -------------[00(01|10)11]-------------------------------------= ----

Billy Wayne McCann, Ph.D.
Google+
PGP K= ey
ir= c://irc.freenode.net:bwayne

MzM0LTcwMy0wMTIyCg=3D=3D | base64


"A rich man will always desire what his wealth cannot acquire." ~= Faust (Goethe)

-------------------------------------= -----[11(10|01)00]---------------------= ---------------------


On Tue, Feb 25, 2014 at 4:15 AM, Mark An= drew Blitz m.blitz%a%leeds.ac.uk <owner-chemistry:ccl.net> wrote:

Sent to CCL by: "Mark Andrew Blitz" [m.blitz\a/leeds.ac.uk]
Dear Colleagues,

On behalf of the MESMER team, I am delighted to announce that MESMER 3.0 (Master Equation Solver for Multi Energy-well Reactions) is now available f= or
download.

The Windows installer and Linux tar file are located at:

http:= //sourceforge.net/projects/mesmer/

The source can also be viewed and downloaded from this site. There are also=
bug and feature request tracking facilities which we encourage you to use.<= br>
The following new features have been incorporated:
=C2=A0Extension of experimental specification to include bath gas.
=C2=A0The ability to analyse Hessian matrices to exclude internal rotor mod= es
prior to the determination of vibrational frequencies.
=C2=A0Addition of a new reaction type =C2=A0pseudo isomerization.
=C2=A0Analytical representation of rate coefficients using Chebyshev polyno= mials
in Cantera and Chemkin formats.
=C2=A0XML Schema support to assist with input file specification.

If you have any comments or suggestions, please dont hesitate to let us
know, either through the above site or by email (Mark Blitz
(M.Blitz/a\leeds.ac.uk= ), Robin Shannon(r.shannon/a\leeds.ac.uk) and Struan
Robertson (Struanhrobertson/a\gmail.com) would be very happy to receive
feedback).

We have recently published an article that describes some of the
implementation details of MESMER (Journal of Physical Chemistry A, 95459560= ,
116 (2012)).

More information is available at the MESMER website:
http:= //www.chem.leeds.ac.uk/mesmer.html

The MESMER team also participate in the MEIC (Master Equation Inter-
Comparison), details of which are available from Prof. John Barker
(jrbarker/a\umich.edu).<= br>

With best regards,

Mark Blitz



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



--001a11c214de3ea6b004f33b6110-- From owner-chemistry@ccl.net Tue Feb 25 10:32:01 2014 From: "Anthony Duben ajdubenprof^yahoo.com" To: CCL Subject: CCL: Windows 8 Compatibility of Abalone Molecular Mechanics Software Message-Id: <-49803-140225072836-24523-PWlqtuVU/ZAyH9JH3gU5EA a server.ccl.net> X-Original-From: Anthony Duben Content-Type: multipart/alternative; boundary="-1480336445-1639910936-1393331310=:65362" Date: Tue, 25 Feb 2014 04:28:30 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Anthony Duben [ajdubenprof-$-yahoo.com] ---1480336445-1639910936-1393331310=:65362 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Abalone is a Molecular Mechanics Software open source project on sourceforg= e.net.=A0 Its primary use is for=0Astudying macromolecular systems, esp. pe= ptides, by molecular mechanics, molecular dynamics, and monte=0Acarlo.=A0 I= t seems to work satisfactorily on Windows XP and Windows 7.=A0 However, I h= ave a student who =0A=0Atried to install it on his Windows 8 Laptop (his on= ly computer).=A0 It installs, but when he starts the program, it=0Acrashes.= =A0 Even after uninstalling, and reinstalling a fresh copy, it crashes.=A0 = He is using the simpler version=0Afor serial CPU's, not the one with GPU li= braries and other bells and whistles.=A0=A0 He has tried to use the =0A=0AW= indows compatibility box settings to no avail.=0A=0AHave others tried to us= e Abalone on a Windows 8 box?=A0 Successfully or unsuccessfully?=A0 (IMHO, = Windows 8=0Ais an abomination.=A0 Looks like a Fisher-Price toy and seems t= o run like one.=A0 I have tried working with my =0A=0Astudent's computer.= =A0 I never know where I am in the operating system.)=0A=0AAJD=0A=0A=A0=0A= =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=0A=0A=0AAnthony J. Duben=0AStephen F. Austin State University=0AP.O.= Box 13006 SFA Station =0A124 Mathematics Building=0ANacogdoches, TX 75962-= 3006=0Aphone: 936-468-1568=0Afax: 936-468-7634=0Ae-mail: dubenaj(a)sfasu.edu= =0Aajdubenprof(a)yahoo.com ---1480336445-1639910936-1393331310=:65362 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Abalone is a Molecular Mechanics Software open sou= rce project on sourceforge.net.  Its primary use is for
studying macromolecular systems, = esp. peptides, by molecular mechanics, molecular dynamics, and monte=
carlo.  It seems to = work satisfactorily on Windows XP and Windows 7.  However, I have a st= udent who
t= ried to install it on his Windows 8 Laptop (his only computer).  It in= stalls, but when he starts the program, it
crashes.  Even after uninstalling, and reinsta= lling a fresh copy, it crashes.  He is using the simpler version
for serial CPU's, not th= e one with GPU libraries and other bells and whistles.   He has t= ried to use the
Windows compatibility box settings to no avail.

Have others tried to use Abalone on a Windows 8 bo= x?  Successfully or unsuccessfully?  (IMHO, Windows 8
is an abomination.  Looks like a Fisher-Price toy and seems to run like one.  I have trie= d working with my
student's computer.  I never know where I am in the operating syst= em.)

AJD
&nb= sp;
=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


Anthony J. Duben
Step= hen F. Austin State University
P.O. Box 13006 SFA Station
124 Mathematics Building
Nacogdoches, TX 75962-3006
phon= e: 936-468-1568
fax: 936-468-7634
e-mail: dubenaj(a)sfasu.edu
ajdube= nprof(a)yahoo.com
---1480336445-1639910936-1393331310=:65362-- From owner-chemistry@ccl.net Tue Feb 25 14:03:00 2014 From: "Tamer sabry t_sabry2005()hotmail.com" To: CCL Subject: CCL: Crystal doping using CATEP Message-Id: <-49804-140225140132-8819-ETc9kVj+VqHwexQEb/3djg%%server.ccl.net> X-Original-From: "Tamer sabry" Date: Tue, 25 Feb 2014 14:01:31 -0500 Sent to CCL by: "Tamer sabry" [t_sabry2005-$-hotmail.com] Dear colleagues of CCL regarding crystal doping using CASTEP code of Material studio, could someone help by clarifying the following: I. For the n-type doping , if the dopant is higher valence than the origin metal, i.e. if i will replace X of valence electron =1 by Y of valence electron= 2, which charge should be applied 0 or -1 or +1 in CASTEP set up as a net charge of the crystal system? II. are the Fermi level should be in a certain position between CB and VB? III. how the effective mass value/position be calculated or obtained? Many thanks in advance Tamer sabry t_sabry2005###hotmail.com From owner-chemistry@ccl.net Tue Feb 25 14:59:00 2014 From: "Bellifa Khadidja kbellifa{}yahoo.com" To: CCL Subject: CCL:G: Windows 8 Compatibility of Abalone Molecular Mechanics Software Message-Id: <-49805-140225115217-29967-DQzx0McggNhffU1SgV3iQA-*-server.ccl.net> X-Original-From: Bellifa Khadidja Content-Type: multipart/alternative; boundary="-1470824145-743465516-1393347117=:40363" Date: Tue, 25 Feb 2014 16:51:57 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: Bellifa Khadidja [kbellifa]|[yahoo.com] ---1470824145-743465516-1393347117=:40363 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear collegues, the toxicity/activity of a molecule depends on the penetrat= ion, the electronic and the steric effect.=0A=A0what are the descriptors to= describe the steric effect in a molecule? is there a descriptor which can = calculated using the Gaussian software.=0Awhat is the best method (experime= ntal, theoritical) to obtain the molecular shape index?=0ASincerely yours= =0A=0A=0A=0A=0ALe Mardi 25 f=E9vrier 2014 17h12, Anthony Duben ajdubenprof^= yahoo.com a =E9crit :=0A =0AAbalone is a Molecula= r Mechanics Software open source project on sourceforge.net.=A0 Its primary= use is for=0Astudying macromolecular systems, esp. peptides, by molecular = mechanics, molecular dynamics, and monte=0Acarlo.=A0 It seems to work satis= factorily on Windows XP and Windows 7.=A0 However, I have a student who =0A= =0Atried to install it on his Windows 8 Laptop (his only computer).=A0 It i= nstalls, but when he starts the program, it=0Acrashes.=A0 Even after uninst= alling, and reinstalling a fresh copy, it crashes.=A0 He is using the simpl= er version=0Afor serial CPU's, not the one with GPU libraries and other bel= ls and whistles.=A0=A0 He has tried to use the =0A=0AWindows compatibility = box settings to no avail.=0A=0AHave others tried to use Abalone on a Window= s 8 box?=A0 Successfully or unsuccessfully?=A0 (IMHO, Windows 8=0Ais an abo= mination.=A0 Looks like a Fisher-Price toy and seems to run like one.=A0 I = have tried working with my =0A=0Astudent's computer.=A0 I never know where = I am in the operating system.)=0A=0AAJD=0A=0A=A0=0A=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=0A=0A=0AAnthony J= . Duben=0AStephen F. Austin State University=0AP.O. Box 13006 SFA=0A Statio= n =0A124 Mathematics Building=0ANacogdoches, TX 75962-3006=0Aphone: 936-468= -1568=0Afax: 936-468-7634=0Ae-mail: dubenaj]![sfasu.edu=0Aajdubenprof]![yah= oo.com ---1470824145-743465516-1393347117=:40363 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear collegues, the t= oxicity/activity of a molecule depends on the penetration, the electronic a= nd the steric effect.
 what are the descriptors to describe the ste= ric effect in a molecule? is there a descriptor which can calculated using = the Gaussian software.
what is the best method (experimental, theoritica= l) to obtain the molecular shape index?
Sincerely yours


Le Mardi 25 f=E9vrier 2014 17h12, Anthony Duben ajdubenprof^ya= hoo.com <owner-chemistry__ccl.net> a =E9crit :
Abalo= ne is a Molecular Mechanics Software open source project on sourceforge.net= .  Its primary use is for
carlo.  It seems to work satisfactorily on Windows XP and = Windows 7.  However, I have a student who
tried to install it on his Windows 8= Laptop (his only computer).  It installs, but when he starts the prog= ram, it
crashes.  = Even after uninstalling, and reinstalling a fresh copy, it crashes.  H= e is using the simpler version
Windows compatibility box settings to no avail.

Have others tried to use Abalone on a Windows 8 box? = ; Successfully or unsuccessfully?  (IMHO, Windows 8
is an abomination. =0A Looks like a = Fisher-Price toy and seems to run like one.  I have tried working with= my
student's comp= uter.  I never know where I am in the operating system.)
<= div style=3D"color:rgb(0, 0, 0);font-size:16px;font-family:HelveticaNeue, H= elvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;background-color= :transparent;font-style:normal;">
AJD
 
=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
=


Anthony J. Duben
Stephen F. Austin State Univers= ity
P.O. Box 13006 SFA=0A Station
124 Mathematics Building
Nacogd= oches, TX 75962-3006
phone: 936-468-1568
fax: 936-468-7634
e-mail:= dubenaj]![sfasu.edu
ajdubenprof]![yahoo.com

=
---1470824145-743465516-1393347117=:40363-- From owner-chemistry@ccl.net Tue Feb 25 15:34:00 2014 From: "Lance Westerhoff lance*|*quantumbioinc.com" To: CCL Subject: CCL: Announcement: QuantumBio Release of QM-based X-ray Crystallography Plugin v1.0 for Phenix Message-Id: <-49806-140225133201-5996-N7CdpzYbA2BowA1QP3ZusQ%server.ccl.net> X-Original-From: Lance Westerhoff Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Tue, 25 Feb 2014 13:31:46 -0500 Mime-Version: 1.0 (Apple Message framework v1283) Sent to CCL by: Lance Westerhoff [lance+*+quantumbioinc.com] Hello All- We are pleased to announce the release of our linear scaling, quantum mechanics DivCon Discovery Suite plug-in v1.0 for the Phenix, x-ray crystallography platform. As was detailed in the recent Phenix Newsletter, when this plugin is installed, the conventional refinement functional along with the stereochemical restraints or CIFile for the ligand(s) and for the surrounding active site(s) are replaced with QM data in "real time" during the refinement in order to increase structural accuracy and decrease artificial strain. To see the full press release along with references and links for further information, please take a look at the following website: http://www.quantumbioinc.com/news/show/PhenixAnnouncement To encourage adoption, we have waived the license fee for non-profit, academic use and we have posted our commercial evaluation license as well. These licenses are available at the following link: http://www.quantumbioinc.com/products/software_licensing Certainly, let me know if you have any questions or if you would like to try out the technology on your own structures! -Lance ____________________ Lance M. Westerhoff, Ph.D. President and General Manager QuantumBio Inc. WWW: http://www.quantumbioinc.com Email: lance[a]quantumbioinc.com From owner-chemistry@ccl.net Tue Feb 25 20:57:00 2014 From: "William F. Polik polik++hope.edu" To: CCL Subject: CCL: BCCE Symposium on Educational Uses of Computational Chemistry and Visualization Message-Id: <-49807-140225201243-6551-4xIIq3+8jSdlpFmX8A36fg!=!server.ccl.net> X-Original-From: "William F. Polik" Content-Type: multipart/alternative; boundary="------------010500010700090101090702" Date: Tue, 25 Feb 2014 20:12:35 -0500 MIME-Version: 1.0 Sent to CCL by: "William F. Polik" [polik|,|hope.edu] This is a multi-part message in MIME format. --------------010500010700090101090702 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Dear CCL'ers, Will you be attending the 2014 Biennial Conference on Chemical Education (BCCE 2014)? If so, please consider submitting an abstract to a symposium on *"Creative Uses of Computational Chemistry and Visualization in the Undergraduate Curriculum"*. The symposium will highlight activities that involve chemical modeling, visualization, simulation, mathematical software, and other computational methods. Course-specific examples as well as efforts that integrate computation throughout the curriculum will be included. BCCE 2014 is being held August 3-7, 2014 at Grand Valley State University in Allendale, Michigan. Conference details are available at http://www.bcce2014.org/ The symposium on Computational Chemistry and Visualization is being co-organized by Shawn Sendlinger (North Carolina Central University), Trilisa Perrine (Ohio Northern University), JR Schmidt (University of Wisconsin, Madison), and myself. The deadline for submitting abstracts is this *Friday, February 28, 2014*. Submissions are being accepted at http://bcce-submissions.com/ Please submit an abstract describing how you use computational chemistry and/or visualization in your curriculum. Thank you! Will Polik Hope College -- ------------------------------------------------------------------------ Dr. William F. Polik Hofma Professor of Chemistry and Chairperson Department of Chemistry Schaap Science Center 2122 Hope College 35 East 12th Street Holland, MI 49422-9000 USA polik,,hope.edu http://www.chem.hope.edu/~polik tel: (616) 395-7639 fax: (616) 395-7118 ------------------------------------------------------------------------ --------------010500010700090101090702 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear CCL'ers,

Will you be attending the 2014 Biennial Conference on Chemical Education (BCCE 2014)?

If so, please consider submitting an abstract to a symposium on "Creative Uses of Computational Chemistry and Visualization in the Undergraduate Curriculum".  The symposium will highlight activities that involve chemical modeling, visualization, simulation, mathematical software, and other computational methods.  Course-specific examples as well as efforts that integrate computation throughout the curriculum will be included.

BCCE 2014 is being held August 3-7, 2014 at Grand Valley State University in Allendale, Michigan.  Conference details are available at
    http://www.bcce2014.org/
The symposium on Computational Chemistry and Visualization is being co-organized by Shawn Sendlinger (North Carolina Central University), Trilisa Perrine (Ohio Northern University), JR Schmidt (University of Wisconsin, Madison), and myself.  The deadline for submitting abstracts is this Friday, February 28, 2014.  Submissions are being accepted at
    http://bcce-submissions.com/

Please submit an abstract describing how you use computational chemistry and/or visualization in your curriculum.  Thank you!

Will Polik
Hope College


--
Dr. William F. Polik
Hofma Professor of Chemistry and Chairperson

Department of Chemistry
Schaap Science Center 2122
Hope College
35 East 12th Street
Holland, MI  49422-9000
USA

polik,,hope.edu
http://www.chem.hope.edu/~polik
tel: (616) 395-7639
fax: (616) 395-7118
--------------010500010700090101090702-- From owner-chemistry@ccl.net Tue Feb 25 23:18:00 2014 From: "RICHARD WOOD rwoodphd#msn.com" To: CCL Subject: CCL:G: Windows 8 Compatibility of Abalone Molecular Mechanics Software Message-Id: <-49808-140225213023-25573-DOdPtMNg4UTE9qECz8C22w-x-server.ccl.net> X-Original-From: RICHARD WOOD Content-Type: multipart/alternative; boundary="_4aae03f6-3e79-4ec8-8641-1e8d8ba3035c_" Date: Tue, 25 Feb 2014 20:30:16 -0600 MIME-Version: 1.0 Sent to CCL by: RICHARD WOOD [rwoodphd(0)msn.com] --_4aae03f6-3e79-4ec8-8641-1e8d8ba3035c_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Steric =3D van der Waals energy. > From: owner-chemistry,ccl.net To: rwoodphd,msn.com Subject: CCL:G: Windows 8 Compatibility of Abalone Molecular Mechanics Soft= ware Date: Tue=2C 25 Feb 2014 16:51:57 +0000 Dear collegues=2C the toxicity/activity of a molecule depends on the penetr= ation=2C the electronic and the steric effect. what are the descriptors to describe the steric effect in a molecule? is t= here a descriptor which can calculated using the Gaussian software. what is the best method (experimental=2C theoritical) to obtain the molecul= ar shape index? Sincerely yours =20 =20 Le Mardi 25 f=E9vrier 2014 17h12=2C Anthony Duben ajdubenprof^yahoo.co= m a =E9crit : Abalone is a Molecular Mechanics Software open source project on source= forge.net. Its primary use is forstudying macromolecular systems=2C esp. p= eptides=2C by molecular mechanics=2C molecular dynamics=2C and montecarlo. = It seems to work satisfactorily on Windows XP and Windows 7. However=2C I= have a student who=20 tried to install it on his Windows 8 Laptop (his only computer). It instal= ls=2C but when he starts the program=2C itcrashes. Even after uninstalling= =2C and reinstalling a fresh copy=2C it crashes. He is using the simpler v= ersionfor serial CPU's=2C not the one with GPU libraries and other bells an= d whistles. He has tried to use the=20 Windows compatibility box settings to no avail. Have others tried to use Abalone on a Windows 8 box? Successfully or unsuc= cessfully? (IMHO=2C Windows 8is an abomination. =0A= Looks like a Fisher-Price toy and seems to run like one. I have tried wor= king with my=20 student's computer. I never know where I am in the operating system.) AJD =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 Anthony J. Duben Stephen F. Austin State University P.O. Box 13006 SFA=0A= Station=20 124 Mathematics Building Nacogdoches=2C TX 75962-3006 phone: 936-468-1568 fax: 936-468-7634 e-mail: dubenaj]![sfasu.edu ajdubenprof]![yahoo.com = --_4aae03f6-3e79-4ec8-8641-1e8d8ba3035c_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Steric =3D van der Waals energy.=

From: owner-chemistry,ccl.net
To: r= woodphd,msn.com
Subject: CCL:G: Windows 8 Compatibility of Abalone Molec= ular Mechanics Software
Date: Tue=2C 25 Feb 2014 16:51:57 +0000

<= div style=3D"color:#000=3Bbackground-color:#fff=3Bfont-family:times new rom= an=2C new york=2C times=2C serif=3Bfont-size:10pt=3B">Dear collegues=2C the= toxicity/activity of a molecule depends on the penetration=2C the electron= ic and the steric effect.
 =3Bwhat are the descriptors to describe t= he steric effect in a molecule? is there a descriptor which can calculated = using the Gaussian software.
what is the best method (experimental=2C th= eoritical) to obtain the molecular shape index?
Sincerely yours


Le Mardi 25 f=E9vrier 2014 17h12= =2C Anthony Duben ajdubenprof^yahoo.com <=3Bowner-chemistry:+:ccl.net>= =3B a =E9crit :
Abalone is a Mol= ecular Mechanics Software open source project on sourceforge.net. =3B I= ts primary use is for
studying macromolecular systems=2C esp. peptides=2C = by molecular mechanics=2C molecular dynamics=2C and monte
carlo. =3B I= t seems to work satisfactorily on Windows XP and Windows 7. =3B However= =2C I have a student who
tried to install it on his Windows 8 Laptop = (his only computer). =3B It installs=2C but when he starts the program= =2C it
crashes. =3B Even after uninstalling=2C and reinstalling a fres= h copy=2C it crashes. =3B He is using the simpler version
<= div style=3D"color:rgb(0=2C 0=2C 0)=3Bfont-size:16px=3Bfont-family:Helvetic= aNeue=2C Helvetica Neue=2C Helvetica=2C Arial=2C Lucida Grande=2C sans-seri= f=3Bbackground-color:transparent=3Bfont-style:normal=3B">for serial C= PU's=2C not the one with GPU libraries and other bells and whistles. = =3B =3B He has tried to use the
Windows compatibility box setting= s to no avail.

Have others tried to use Abalone on a Windows 8 box= ? =3B Successfully or unsuccessfully? =3B (IMHO=2C Windows 8=
is an= abomination. =3B=0A= Looks like a Fisher-Price toy and seems to run like one. =3B I have tr= ied working with my
student's computer. =3B I never know where = I am in the operating system.)

AJD
 =3B
=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


Anthony J. Duben
Stephen F.= Austin State University
P.O. Box 13006 SFA=0A= Station
124 Mathematics Building
Nacogdoches=2C TX 75962-3006
ph= one: 936-468-1568
fax: 936-468-7634
e-mail: dubenaj]![sfasu.edu
aj= dubenprof]![yahoo.com


=
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