From owner-chemistry@ccl.net Fri May 1 00:42:01 2009 From: "Kshatresh Dutta Dubey kshatresh],[gmail.com" To: CCL Subject: CCL: Docking Problem Message-Id: <-39213-090501004051-12649-HUq3QXMh9NW7QOz4W67wCQ**server.ccl.net> X-Original-From: Kshatresh Dutta Dubey Content-Type: multipart/alternative; boundary=000e0cd4043403a1a40468d26abe Date: Fri, 1 May 2009 10:10:37 +0530 MIME-Version: 1.0 Sent to CCL by: Kshatresh Dutta Dubey [kshatresh=-=gmail.com] --000e0cd4043403a1a40468d26abe Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Vincent, Firstly thanks for reply, in my previous question i got different docking score by docking other ligands in virtual and induced fit. The docking scores are similar for only a particular ligand. On Thu, Apr 30, 2009 at 5:25 PM, Vincent.Leroux[A]loria.fr < owner-chemistry ~~ ccl.net> wrote: > > Sent to CCL by: Vincent.Leroux(0)loria.fr > Probably that you ended up with the same docked conformation in both case= s. > > > "Kshatresh Dutta Dubey kshatresh . gmail.com" > a =E9crit : > > Dear subscribers , >> i have docked a ligand into a protein by both virtual docking as well a= s >> induced fit and got same docking score. What does this result >> signifiy????? >> >> thanks in advance >> Kshatresh dutta dubey >> >> > > > - This is automatically added to each message by the mailing script -http://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --000e0cd4043403a1a40468d26abe Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Dear Vincent,
Firstly thanks for reply, i= n my previous question i got different docking score by docking other=A0 li= gands in virtual and induced fit. The docking scores are similar for only a= particular ligand.
On Thu, Apr 30, 2009 at 5:25 PM, Vinc= ent.Leroux[A]loria.fr <= ;owner-chemistry ~~ ccl.net>= wrote:

Sent to CCL by: Vincent.Leroux(0)loria.fr
Probably that you ended up with the same docked conformation in both cases.=


"Kshatresh Dutta Dubey kshatresh . gmail.com" <owner-chemistry|,|ccl.net> a =E9crit=A0:


Dear subscribers ,
=A0i have docked a ligand into a protein by both virtual docking as well as=
induced fit and =A0got same docking score. What does this result signifiy??= ???

=A0thanks in advance
Kshatresh dutta dubey




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--000e0cd4043403a1a40468d26abe-- From owner-chemistry@ccl.net Fri May 1 01:29:01 2009 From: "Babak Khalili khalili.babak||gmail.com" To: CCL Subject: CCL: Error link 716 Message-Id: <-39214-090501012728-4295-TlvjoS31L143hi97Y8/JiA*_*server.ccl.net> X-Original-From: Babak Khalili Content-Type: multipart/alternative; boundary=001636c599a3d4dc140468d31085 Date: Fri, 1 May 2009 09:57:16 +0430 MIME-Version: 1.0 Sent to CCL by: Babak Khalili [khalili.babak*o*gmail.com] --001636c599a3d4dc140468d31085 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear subscribers, I decieded to calcuate freq command in solvent, but after 20 min the l716 occures it means" Processes information for optimizations and frequencies". May you help me what can I do? Babak Khalili, PhD candidate of Biochemistry --001636c599a3d4dc140468d31085 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear subscribers,
I decieded to calcuate freq command in solvent, but after 20 min the l716 occures it means" Processes information for optimizations and frequencies". May you help me what can I do?

Babak Khalili,
PhD candidate of Biochemistry
--001636c599a3d4dc140468d31085-- From owner-chemistry@ccl.net Fri May 1 06:28:01 2009 From: "Kikuo Harigaya harigaya|*|gmail.com" To: CCL Subject: CCL: Graphene: Theory and Experiment Message-Id: <-39215-090501062549-2713-yr8bpWrS2E1IMva4vjgFuw|a|server.ccl.net> X-Original-From: Kikuo Harigaya Content-Type: multipart/alternative; boundary=0016364ec86875ec7e0468d6ca32 Date: Fri, 1 May 2009 18:53:55 +0900 MIME-Version: 1.0 Sent to CCL by: Kikuo Harigaya [harigaya() gmail.com] --0016364ec86875ec7e0468d6ca32 Content-Type: text/plain; charset=ISO-8859-7 Content-Transfer-Encoding: quoted-printable Dear Collegues This is further information. If you submit your short abstract, please Cc: to me. Also, please submit your proceeding paper to me by August 25, 2009. The max. pages are 4 pages. If you submit your short-abstract, please do not forget to quote the symposium number "No.13". Schedule might be tight more than the home page announce. Regards, *** The short circular can be found at: http://staff.aist.go.jp/k.harigaya/doc/short%20circular.pdf International Symposium "From Open-Shell Conjugated Molecules to Graphene: Theory and Experiment" International symposium on electronic properties in graphene, nanographene, and open-shell conjugated systems, will be held in the conference: "Seventh International Conference of Computational Methods in Sciences and Engineering" (http://www.iccmse.org/) at Hotel Rodos Palace, Rodos, Crete, Greece. The conference period will be September 29 - October 4, 2009. Submission of the short abstract is welcome for interested persons. See the details at the Web site: http://www.iccmse.org/. Scope "Graphene" - a new carbonaceous material - is distinguished from conventional electronic systems such as graphite due to its exceptional features, e.g., a large magnetic moment around the zigzag edges and massles= s Dirac fermion, stimulating development of future electronic/spintronic devices. Several unique features of graphene are closely connected with the "open-shell character", which originates in the "instability of chemical bonds" in =F0-conjugated system with unconventional spin states and strongl= y correlates with the topology of =F0-electron array, especially aromatic sex= tet formation. This symposium focuses on recent hot topics regarding unique physical and chemical properties derived from pseudo and real spins in =F0-conjugated compounds, toward collaboration between theory, computationa= l modeling and experiment. A wide range of compounds from small conjugated/aromatic molecules and inorganic metal complexes to nano- and large-size graphenes will be covered, and origin of the open-shell characte= r as well as functional properties such as electron conductivity, optical and magnetic properties will be concentrated as important domains in the symposium. Organizers Kikuo Harigaya, AIST; Masayoshi Nakano, Osaka University; Takashi Kubo, Osaka University Contact Kikuo Harigaya, AIST; Tel: 029-861-5151; FAX: 029-861-5375; E-mail: k.harigaya]|[aist.go.jp --=20 Dr. Kikuo Harigaya Address: Nanotechnology Research Institute, AIST, Tsukuba 305-8568, Japan TEL: +81-29-861-5151, FAX: +81-29-861-5375 URL: http://staff.aist.go.jp/k.harigaya/ --0016364ec86875ec7e0468d6ca32 Content-Type: text/html; charset=ISO-8859-7 Content-Transfer-Encoding: quoted-printable Dear Collegues

This is further information.  If you submit
y= our short abstract, please Cc: to me.

Also, please submit your proce= eding paper
to me by August 25, 2009.  The max.  pages
are = 4  pages.

If you submit your short-abstract, please
do not forget to quote the= symposium
number "No.13".

Schedule might be tight more= than the home
page announce.

Regards,

***

The shor= t circular can be found at:
htt= p://staff.aist.go.jp/k.harigaya/doc/short%20circular.pdf

Interna= tional Symposium "From Open-Shell Conjugated Molecules to Graphene: Th= eory and Experiment"
International symposium on electronic properties in graphene, nanographene,= and open-shell conjugated systems, will be held in the conference: "S= eventh International Conference of Computational Methods in Sciences and En= gineering" (http://www.iccmse.org/<= /a>) at Hotel Rodos Palace, Rodos, Crete, Greece. The conference period wil= l be September 29 - October 4, 2009. Submission of the short abstract is we= lcome for interested persons. See the details at the Web site: http://www.iccmse.org/.

Scope
"Graphene" – a new carbonaceous material &ndas= h; is distinguished from conventional electronic systems such as graphite d= ue to its exceptional features, e.g., a large magnetic moment around the zi= gzag edges and massless Dirac fermion, stimulating development of future el= ectronic/spintronic devices. Several unique features of graphene are closel= y connected with the "open-shell character", which originates in = the "instability of chemical bonds" in =F0-conjugated system with= unconventional spin states and strongly correlates with the topology of = =F0-electron array, especially aromatic sextet formation. This symposium fo= cuses on recent hot topics regarding unique physical and chemical propertie= s derived from pseudo and real spins in =F0-conjugated compounds, toward co= llaboration between theory, computational modeling and experiment. A wide r= ange of compounds from small conjugated/aromatic molecules and inorganic me= tal complexes to nano- and large-size graphenes will be covered, and origin= of the open-shell character as well as functional properties such as elect= ron conductivity, optical and magnetic properties will be concentrated as i= mportant domains in the symposium.

Organizers
Kikuo Harigaya, AIST; Masayoshi Nakano, Osaka University;= Takashi Kubo, Osaka University

Contact
Kikuo Harigaya, AIST; Tel= : 029-861-5151; FAX: 029-861-5375; E-mail: k.harigaya]|[aist.go.jp

--

Dr. Kikuo Harigaya
Address: Nanotechnology Research Insti= tute,
AIST, Tsukuba 305-8568, Japan
TEL: +81-29-861-5151, FAX: +81-29= -861-5375
URL: http://st= aff.aist.go.jp/k.harigaya/
--0016364ec86875ec7e0468d6ca32-- From owner-chemistry@ccl.net Fri May 1 07:46:00 2009 From: "Stephen.Garrison]=[srnl.doe.gov" To: CCL Subject: CCL: One unpaired electron - Zero integrated spin density? Message-Id: <-39216-090501074444-1458-dM9ws74t6jBB00yOO4sZrQ###server.ccl.net> X-Original-From: Stephen.Garrison*|*srnl.doe.gov Content-Type: multipart/alternative; boundary="=_alternative 0040813C852575A9_=" Date: Fri, 1 May 2009 07:44:34 -0400 MIME-Version: 1.0 Sent to CCL by: Stephen.Garrison~!~srnl.doe.gov This is a multipart message in MIME format. --=_alternative 0040813C852575A9_= Content-Type: text/plain; charset="US-ASCII" Could someone explain to me how a system can have one unpaired electron, but nearly zero integrated spin density? I am using CASTEP (LDA functional) and am working on a periodic metallic system with 189 electrons. I start the calculation with an estimate of 5 unpaired electrons. The SCF convergence cycle for the initial geometry finds a solution with the following spin densities: 2*Integrated Spin Density = -0.533909E-01 2*Integrated |Spin Density| = 0.972315 The final, optimized geometry has the following spin densities: 2*Integrated Spin Density = -0.337735E-03 2*Integrated |Spin Density| = 0.612583E-02 This does not make much physical sense to me. How can a system have an unpaired electron but zero integrated absolute value(spin density)? What am I missing? Thanks for you help and clarification. Stephen -- Stephen L. Garrison, Ph.D. Senior Engineer Engineering Modeling and Simulation Savannah River National Laboratory Savannah River Site 773-42A, Room 181 Aiken, SC 29808 803-725-2404 Stephen.Garrison]|[SRNL.doe.gov --=_alternative 0040813C852575A9_= Content-Type: text/html; charset="US-ASCII"
Could someone explain to me how a system can have one unpaired electron, but nearly zero integrated spin density?

I am using CASTEP (LDA functional) and am working on a periodic metallic system with 189 electrons.

I start the calculation with an estimate of 5 unpaired electrons. The SCF convergence cycle for the initial geometry finds a solution with the following spin densities:

 2*Integrated Spin Density   =   -0.533909E-01
 2*Integrated |Spin Density| =    0.972315    

The final, optimized geometry has the following spin densities:

 2*Integrated Spin Density   =   -0.337735E-03
 2*Integrated |Spin Density| =    0.612583E-02

This does not make much physical sense to me. How can a system have an unpaired electron but zero integrated absolute value(spin density)? What am I missing?

Thanks for you help and clarification.

Stephen

--
Stephen L. Garrison, Ph.D.
Senior Engineer
Engineering Modeling and Simulation
Savannah River National Laboratory
Savannah River Site
773-42A, Room 181
Aiken, SC 29808
803-725-2404
Stephen.Garrison]|[SRNL.doe.gov
 --=_alternative 0040813C852575A9_=-- From owner-chemistry@ccl.net Fri May 1 11:26:00 2009 From: "Henry Martinez hmartine^gmail.com" To: CCL Subject: CCL:G: Electron density with Gaussian 03 Message-Id: <-39217-090501111841-28127-rDZ+NNnoYQUAirXSZG9J9w!^!server.ccl.net> X-Original-From: "Henry Martinez" Date: Fri, 1 May 2009 11:18:38 -0400 Sent to CCL by: "Henry Martinez" [hmartine-*-gmail.com] Can any body tell me how to calculate, and make the image of the electron density of a molecule using Gaussian 03. I have both Gaussian view 03 and Gaussian 03. And also, how do I know from two electron density images, of two different molecules, which one is more electron rich? Thanks a lot From owner-chemistry@ccl.net Fri May 1 12:01:00 2009 From: "Henry Martinez hmartine{=}gmail.com" To: CCL Subject: CCL:G: Transition state calculation Message-Id: <-39218-090501112518-28614-P36v8uIzw+zOfOhsGsMwOw|a|server.ccl.net> X-Original-From: "Henry Martinez" Date: Fri, 1 May 2009 11:25:14 -0400 Sent to CCL by: "Henry Martinez" [hmartine##gmail.com] With Gaussian, How do I calculate the transition state of two molecules that are interacting? Then How do I calculate the DeltaG, DeltaH, DeltaS, and finally the Activation energy?, Usually when is a rearrangement of a molecule I calculate the Ground state of the initial structure, and the Transition state minimum, then I can have the DeltaS, G, H and activation energy. But when I have two molecules, I do not know how to do it. Which one of the two molecules should I take to do the calculations of DeltaS, G, H and activation energy. Thanks a lot From owner-chemistry@ccl.net Fri May 1 15:21:01 2009 From: "Yvonne Connolly Martin yvonnecmartin-x-comcast.net" To: CCL Subject: CCL: Prediction of Tautomers Message-Id: <-39219-090501142643-31901-Y1mcJdjh87nID/ukXR2+og ~~ server.ccl.net> X-Original-From: "Yvonne Connolly Martin" Date: Fri, 1 May 2009 14:26:39 -0400 Sent to CCL by: "Yvonne Connolly Martin" [yvonnecmartin^^comcast.net] I am looking for a good review or comparison of quantum chemical methods to predict tautomer ratios. There appear to be hundreds of such applications published, but I have not found a systematic review or comparison of the approach or level of theory needed to provide accurate estimates. Although my interest is in predicting tautomer ratio in water or a macromolecular binding site, any critical references would be appreciated. Comments on QM/MM methods of ligands bound to proteins are also welcome. Thanks, Yvonne Martin yvonnecmartin*comcast.net