From owner-chemistry@ccl.net Thu Jun 23 02:54:01 2011 From: "Sue L chsue2004(0)yahoo.com" To: CCL Subject: CCL:G: Question for CIS frequency calculation Message-Id: <-44957-110623024428-4799-GGoKle6ScL/KW7ArZtvDRA{:}server.ccl.net> X-Original-From: "Sue L" Date: Thu, 23 Jun 2011 02:44:26 -0400 Sent to CCL by: "Sue L" [chsue2004^^^yahoo.com] Dear CCL users I have performed a frequency calculation at the CIS level of theory using Gaussian 03 (64 bit, Linux OS). The calculation was terminated abnormally with the error message Error: _mp_barrier: bad lcpu 2 The last two line of the output shown below G2DrvN: will do 21 centers at a time, making 4 passes doing MaxLOS=2. Calling FoFCou, ICntrl= 3307 FMM=T I1Cent= 0. Does anyone know how to solve the problem? Many thanks for the help. Best regards, Sue From owner-chemistry@ccl.net Thu Jun 23 04:03:00 2011 From: "Mico Leggesse ermiaslegg{}gmail.com" To: CCL Subject: CCL:G: Radical anion Message-Id: <-44958-110623040145-22602-qH/fEtcguGbk5YqyfhQIQg-.-server.ccl.net> X-Original-From: "Mico Leggesse" Date: Thu, 23 Jun 2011 04:01:43 -0400 Sent to CCL by: "Mico Leggesse" [ermiaslegg,gmail.com] Dear All; Can any one tell me how i could locate the additional electron in the radical anion using Gaussian 09 package? also could you tell me how i should proceed if i want to study the addition of one electron to this radical anion? Thank You in advance! From owner-chemistry@ccl.net Thu Jun 23 04:51:01 2011 From: "Anup Thomas anupiict(_)gmail.com" To: CCL Subject: CCL: Regarding DFT HOMO LUMO Vs Cyclic Voltametry HOMO LUMO Message-Id: <-44959-110623044915-2398-+U5AKrJKf0UwziNjq9tGUA- -server.ccl.net> X-Original-From: "Anup Thomas" Date: Thu, 23 Jun 2011 04:49:12 -0400 Sent to CCL by: "Anup Thomas" [anupiict,+,gmail.com] Respected ccl.net users Emperical estimates of HOMO/LUMO = (Eonset + 4.4) eV from the the Cyclic voltametry studies on organic semiconductors are showing better agrement with HOMO/LUMO obtained from DFT (usually B3LYP/631+G(d,p)). But when some. The DFT estimated IP and EA correlate very well, but much better results are obtained > from the Eigen Value. Please discuss regarding this. Regards Anup Thms SRF cc-Lab IICT, Hyderbad From owner-chemistry@ccl.net Thu Jun 23 06:46:00 2011 From: "Sergio Emanuel Galembeck segalemb~~usp.br" To: CCL Subject: CCL:G: Radical anion Message-Id: <-44960-110623064435-14342-uEYk47gkxDFfRNRFQiuIJQ*server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Thu, 23 Jun 2011 07:44:25 -0300 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb*_*usp.br] Dear Mico, The location of the extra electron could be found in the spin density matrix, or density of alpha minus beta electrons. To calculate a radical anion you need to specify charge = -1 and multiplicity = 2. Best regards, Sergio Citando "Mico Leggesse ermiaslegg{}gmail.com" : > > Sent to CCL by: "Mico Leggesse" [ermiaslegg,gmail.com] > Dear All; > Can any one tell me how i could locate the additional electron in the radical > anion using Gaussian 09 package? also could you tell me how i should > proceed if > i want to study the addition of one electron to this radical anion? > Thank You in advance!> > > From owner-chemistry@ccl.net Thu Jun 23 07:27:00 2011 From: "Mauricio Esguerra mauricio.esguerra . gmail.com" To: CCL Subject: CCL: ctDNA Message-Id: <-44961-110623043634-25012-GCUTlXm1ZnD3BSNkVcy55A|*|server.ccl.net> X-Original-From: Mauricio Esguerra Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 23 Jun 2011 10:36:20 +0200 MIME-Version: 1.0 Sent to CCL by: Mauricio Esguerra [mauricio.esguerra^-^gmail.com] Hi Jevah, What about using the structures derived from fiber diffraction data which you can build with the fiber program in the 3DNA suite of programs? e.g., by issuing the following commands once you've installed 3DNA: fiber -1 ADNA.pdb fiber -4 BDNA.pdb fiber -7 CDNA.pdb fiber -17 LDNA.pdb Or which you can also build using the web-interface of 3DNA at: http://w3dna.rutgers.edu Good luck, Mauricio On 06/21/2011 07:57 PM, Close, David M. CLOSED[A]mail.etsu.edu wrote: > > Sent to CCL by: "Close, David M." [CLOSED%a%mail.etsu.edu] > Jevah: > > I am not sure there is a crystal structure of DNA. There are lots of crystal structures of oligomers with good resolution. I think however you will have to look at your hydration levels and decide if you have A or B-DNA, and then find a suitable oligomer structure that has a similar base run that you are interested in. > > Regards, Dave Close. > > -----Original Message----- >> From: owner-chemistry+closed==etsu.edu(~)ccl.net [mailto:owner-chemistry+closed==etsu.edu(~)ccl.net] On Behalf Of Jevahcel Strong jevahcel,hotmail.com > Sent: Tuesday, June 21, 2011 10:40 AM > To: Close, David M. > Subject: CCL: ctDNA > > > Sent to CCL by: "Jevahcel Strong" [jevahcel:hotmail.com] > Hi Folks, > > I am trying to work on the Calf Thymus DNA, but I cannot find its crystal structure. Could anybody please kindly offer me some information regarding this, like pdb entries. > Any of your kind help will be very appreciated > > Sincerely > Jevahhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > From owner-chemistry@ccl.net Thu Jun 23 08:02:00 2011 From: "=?UTF-8?B?546L5bu6QWJib3R0IFdBTkc=?= abbott.cn|gmail.com" To: CCL Subject: CCL:G: Multiple Step Minimization and Energy Job in Gaussian 09 Message-Id: <-44962-110623045133-7551-3vaqPnbq5WNCZfQkWGszWA[]server.ccl.net> X-Original-From: =?UTF-8?B?546L5bu6QWJib3R0IFdBTkc=?= Content-Type: multipart/alternative; boundary=bcaec520ea25b444b804a65d303f Date: Thu, 23 Jun 2011 16:51:26 +0800 MIME-Version: 1.0 Sent to CCL by: =?UTF-8?B?546L5bu6QWJib3R0IFdBTkc=?= [abbott.cn###gmail.com] --bcaec520ea25b444b804a65d303f Content-Type: text/plain; charset=UTF-8 ------------------ - Geometry optimization input file, named as Geom-Opt.com with the check point file named as Geom-Opt.chk. - the following Freq calculation, named as Geom-Freq.com with the check point file named as Geom-Freq.chk. Pls use Geom=Check Guess=Read in the input file. Use the following script. -----------------------cut here---------------- #!/bin/bash g03 /directory/where/you/put/your/files/Geom-Opt.com & wait cp /directory/where/you/put/your/files/Geom-Opt.chk /directory/where/you/put/your/files/Geom-Freq.chk g03 /directory/where/you/put/your/files/Geom-Freq.com & wait -----------------------end here--------------- * * * * * * * **Abbott WANG* State Key Lab of Theoretical & Computational Chemistry Institute of Theoretical Chemistry Jilin University Changchun, 130023 P.R. China Tel.+86-135-9617-5450 Email: abbott.cn#gmail.com On Thu, Jun 23, 2011 at 7:28 AM, Bradley Rose brose,live.com < owner-chemistry-#-ccl.net> wrote: > > Sent to CCL by: "Bradley Rose" [brose#live.com] > Hello > I was wanting to create an input file for Gaussian 09 to run a minimization > and then run a single point energy calculation on the resulting geometry > with one input file since I am calculating energies for a number of > derivatives. I would like to use two different check files if possible. My > attempts have not been successful in all the variations that I have tried, > an example (incorrect) input I have been testing for H2 is shown below > > > %mem=1GB > %chk=H2PM3 > # opt=calcfc freq pm3 geom=connectivity > > PM3 minimization + frequency > > 0 1 > H -2.49523788 -0.29761904 0.00000000 > H -3.09523788 -0.29761904 0.00000000 > > 1 2 1.0 > 2 > > --Link1-- > %mem=1GB > %chk=H2HF > # HF/6-31G(d) geom=read > > SP energy calc > > > Thanks in advance. > Brad Rose > brose,live.com> > > --bcaec520ea25b444b804a65d303f Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
<My solution>
------------------

  • Geometry optimization input file, named a= s Geom-Opt.com with the check point file named as=C2=A0Geom-Opt.c= hk.
  • the following Freq calculation, named as Geom-Freq.com=C2=A0wi= th the check point file named as=C2=A0Geom-Freq.chk. Pls use Geom= =3DCheck Guess=3DRead in the input file.=C2=A0
Use the fo= llowing script.=C2=A0
-----------------------cut here----------------
#!/bin/bas= h
g03 /directory/where/you/put/your/files/Geom-Opt.com &
=
wait
cp=C2=A0= /directory/where/you/put/your/files/Geom-Opt.chk=C2=A0/dire= ctory/where/you/put/your/files/Geom-Freq.chk
g03=C2=A0/directory/where/you/put/your/files/Geom-Fre= q.com &
wait
-----------------------end here---------------=



<= font face=3D"tahoma, sans-serif">


=
Abbott WANG
State Key Lab of Theoretical &a= mp; Computational Chemistry
Institute of Theoretical Chemistry
Jilin University
Changchun, 130023=
P.R. China
Tel.+86-135-9617-5450
Email:=C2=A0abbott.= cn#gmail.com





On Thu, Jun 23, 2011 at 7:28 AM, Bradley= Rose brose,live.com <= owner-chemistry-#-ccl.net><= /span> wrote:

Sent to CCL by: "Bradley =C2=A0Rose" [brose#live.com]
Hello
I was wanting to create an input file for Gaussian 09 to run a minimization= and then run a single point energy calculation on the resulting geometry w= ith one input file since I am calculating energies for a number of derivati= ves. =C2=A0I would like to use two different check files if possible. =C2= =A0My attempts have not been successful in all the variations that I have t= ried, an example (incorrect) input I have been testing for H2 is shown belo= w


%mem=3D1GB
%chk=3DH2PM3
# opt=3Dcalcfc freq pm3 geom=3Dconnectivity

PM3 minimization + frequency

0 1
=C2=A0H =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 -2.49523788= =C2=A0 -0.29761904 =C2=A0 =C2=A00.00000000
=C2=A0H =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 -3.09523788= =C2=A0 -0.29761904 =C2=A0 =C2=A00.00000000

=C2=A01 2 1.0
=C2=A02

--Link1--
%mem=3D1GB
%chk=3DH2HF
# HF/6-31G(d) geom=3Dread

SP energy calc


Thanks in advance.
Brad Rose
brose,live.com



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--bcaec520ea25b444b804a65d303f-- From owner-chemistry@ccl.net Thu Jun 23 08:37:00 2011 From: "Mauricio Esguerra esguerra]^[rci.rutgers.edu" To: CCL Subject: CCL: ctDNA Message-Id: <-44963-110623050806-2820-LaJ3Ien0VqEj/dqtbKbz8g%server.ccl.net> X-Original-From: Mauricio Esguerra Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 23 Jun 2011 11:07:53 +0200 MIME-Version: 1.0 Sent to CCL by: Mauricio Esguerra [esguerra:_:rci.rutgers.edu] Hi Jevah, What about using the structures derived from calf thymus DNA fiber diffraction data which you can build with the fiber program in the 3DNA suite of programs? e.g., by issuing the following commands once you've installed 3DNA: fiber -1 ADNA.pdb fiber -4 BDNA.pdb fiber -7 CDNA.pdb fiber -17 LDNA.pdb Or which you can also build using the web-interface of 3DNA at: http://w3dna.rutgers.edu Good luck, Mauricio > Sent to CCL by: "Jevahcel Strong" [jevahcel:hotmail.com] > Hi Folks, > > I am trying to work on the Calf Thymus DNA, but I cannot find its crystal structure. Could anybody please kindly offer me some information regarding this, like pdb entries. > Any of your kind help will be very appreciated > > Sincerely > Jevah From owner-chemistry@ccl.net Thu Jun 23 09:12:00 2011 From: "Sherin Alfalah shireenfalah ~~ hotmail.com" To: CCL Subject: CCL: starting point to read/learn docking Message-Id: <-44964-110623040543-27061-vWVCzRXQCkhxewZ/S3X8KA^^^server.ccl.net> X-Original-From: "Sherin Alfalah" Date: Thu, 23 Jun 2011 04:05:41 -0400 Sent to CCL by: "Sherin Alfalah" [shireenfalah===hotmail.com] Dear CCL people, I am a computational chemist who wants to learn docking. There are some free software packages with good tutorials but I am wondering which book, reviews, articles can help as starting point to read about (or learn) the theory of docking? All the material I managed to find are "advanced" while I would appreciate any recommendations for more "basic" material. Thanks in advance Best regards Sherin Alfalah email: shireenfalah!^!hotmail.com From owner-chemistry@ccl.net Thu Jun 23 09:46:00 2011 From: "Olasunkanmi Lukman Olawale walecomuk[A]yahoo.co.uk" To: CCL Subject: CCL: Entropy Message-Id: <-44965-110623083928-10987-mfwVfr0dZyhgCH49h2xAQA(0)server.ccl.net> X-Original-From: Olasunkanmi Lukman Olawale Content-Type: multipart/alternative; boundary="0-1611316523-1308832759=:41646" Date: Thu, 23 Jun 2011 13:39:19 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Olasunkanmi Lukman Olawale [walecomuk+/-yahoo.co.uk] --0-1611316523-1308832759=:41646 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable By entropy (S), I assume you mean absolute entropy and not dS (entropy chan= ge). =0AYou are not like to find negative S for a free atom or a compound i= n its =0Astandard state. However, I have come across negative S for aquated= ions. To me, =0Aa reasonable physical interpretation of these values is th= at solvated ions are =0Amore=A0ordered than free ions. Suppose S=3D0 implie= s perfect orderliness, S>0 =0Aimplies less ordered, then S<0 should mean mo= re ordered than (ordinarily) =0Aexpected. The enhanced orderliness is due t= o solvation.=0A=0AOlasunkanmi L.O.=0ADepartment of Chemistry,=0AObafemi Awo= lowo University,=0AIle-Ife, Nigeria.=0A=0A=0A=0A=0A________________________= ________=0AFrom: Bonoit Bonoit bonoit_10%%yahoo.fr =0ATo: "Olasunkanmi, Olawale Lukman " =0ASe= nt: Wed, 22 June, 2011 0:28:13=0ASubject: CCL: Entropy=0A=0A=0ASent to CCL = by: "Bonoit=A0 Bonoit" [bonoit_10[]yahoo.fr]=0AHello everyone,=0AI'm writin= g to enquire about the negative values of the thermodynamic data of =0Aentr= opy (S) for some species especially in aqueous systems.=0AMy question is as= follow;=0AWhy we have this negative sign? i mean what is the origin of thi= s?=0AWhat is the significance of such value of S?=0AIt can be just equal or= greater than zero?=0AThank you.=0ABonoit=0A=0A=0A=0A-=3D This is automatic= ally added to each message by the mailing script =3D-=0ATo recover the emai= l address of the author of the message, please change=0Athe strange charact= ers on the top line to the _-_ sign. You can also=0Alook up the X-Original-Fr= om: line in the mail header.=0A=0AE-mail to subscribers: CHEMISTRY_-_ccl.net = or use:=0A=A0 =A0 =A0=0A=0A==0A=A0 =A0 =A0 ht= tp://www.ccl.net/cgi-bin/ccl/send_ccl_message=0A=0A= =0A=A0 =A0 =A0=0A=0ABefore pos= ting, check wait time at: http://www.ccl.net=0A=0AJob: http://www.ccl.net/j= obs =0AConferences: http://server.ccl.net/chemistry/announcements/conferenc= es/=0A=0ASearch Messages: http://www.ccl.net/chemistry/searchccl/index.shtm= l=0A=0A=0A=A0 =A0 =A0==0A=0ARTFI: http://www.ccl.net/chemistry/ab= outccl/instructions/ --0-1611316523-1308832759=:41646 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
=0A
By entropy (S), I assume you mean absolu= te entropy and not dS (entropy change). You are not like to find negative S= for a free atom or a compound in its standard state. However, I have come = across negative S for aquated ions. To me, a reasonable physical interpreta= tion of these values is that solvated ions are more ordered than free = ions. Suppose S=3D0 implies perfect orderliness, S>0 implies less ordere= d, then S<0 should mean more ordered than (ordinarily) expected. The enh= anced orderliness is due to solvation.
=0A
 
=0A
Ola= sunkanmi L.O.
=0A
Department of Chemistry,
=0A
Obafemi Aw= olowo University,
=0A
Ile-Ife, Nigeria.
=0A

= =0A
From: Bonoit Bonoit bonoit_10%%yahoo.fr <owner-ch= emistry_-_ccl.net>
To: = "Olasunkanmi, Olawale Lukman " <walecomuk_-_yahoo.co.uk>
= Sent: Wed, 22 June, 2011 0:28:= 13
Subject: CCL: Entropy=


Sent to CCL by: "Bonoit  Bonoit" [bonoit_10[]yahoo.= fr]
Hello everyone,
I'm writing to enquire about the negative values = of the thermodynamic data of entropy (S) for some species especially in aqu= eous systems.
My question is as follow;
Why we have this negative sig= n? i mean what is the origin of this?
What is the significance of such v= alue of S?
It can be just equal or greater than zero?
Thank you.
B= onoit



-=3D This is automatically added to each message by th= e mailing script =3D-the strange characters on t= he top line to the _-_ sign. You can also
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--0-1611316523-1308832759=:41646-- From owner-chemistry@ccl.net Thu Jun 23 13:08:00 2011 From: "Rakesh Kumar rakesh.kumar|execs.com" To: CCL Subject: CCL: HTS of compounds libraries using ONTOMINE Message-Id: <-44966-110623130618-9593-q4FDFhQhG0FXpa+wXfOsug%server.ccl.net> X-Original-From: "Rakesh Kumar" Date: Thu, 23 Jun 2011 13:06:16 -0400 Sent to CCL by: "Rakesh Kumar" [rakesh.kumar#%#execs.com] Dear CCLers, I would like to introduce you to our novel Chemoinformatics software known as "ONTOMINE" ONTOMINE is transforming the structural information for chemically, biologically or pharmacologically related molecules to a hierarchical schema of concepts and descriptors. ONTOMINE discovers patterns in the related schema and predicts biological activity, using rules inferred from analyzing the patterns. One significant advantage of ONTOMINE is that they enable scaffold hopping, since the core scaffold is not conserved when patterns characteristic of an activity is discovered. ONTOMINE screen compounds libraries for :- 1. Drug targets ( Enzyme, receptors, ion channel, growth factor etc. ) 2. Biological processes ( e.g. adjuvant, alkaloid, anti-spasmodic, reducing agents etc.) 3. Therapeutic areas ( Anti Allergic, Anti cancer, Anti infective, Anti- Inflammatory etc.) 4. Toxicity (systemic, organ specific and genetic) and side effect prediction using Ontomine Tox module. Example include hepatotoxicity, mutagenecity, and QT elongation. 5. ADME and physicochemical property prediction (including logS, logP, logD, pKa) using Ontomine ADME module. Scaffold hopping prediction for finding new isofunctional chemotypes. I'd also request you to visit http://www.sbw.fi/ontomine for more information regarding ONTOMINE. Please let me know if ONTOMINE interests you. I'd be happy to organize a web- demonstration for you. Thanks Best Regards Rakesh Kumar ----------------------- SBW Ltd. Ph :- +919810448375 Email :- rakesh.kumar(0)sbw.fi Skype :- rakesh.kumar-sbw.fi Web :- www.sbw.fi From owner-chemistry@ccl.net Thu Jun 23 14:36:01 2011 From: "Mikael Johansson mikael.johansson]=[iki.fi" To: CCL Subject: CCL:G: Radical anion Message-Id: <-44967-110623143346-11745-LiNnJljaR6JbBZf5SHWukg : server.ccl.net> X-Original-From: Mikael Johansson Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Thu, 23 Jun 2011 21:33:19 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson^iki.fi] Dear Sergio and All, The spin density difference between a neutral and anionic species is _not_ in general a good measure of "where" the added electron got distributed. Instead, one should look directly at the total charge density difference. Especially with metal atoms in the system, the differences between spin density and charge density of neutral/anion can be very different. Of course, the original poster might actually be interested in the spin density, and not the charge density difference... Have a good midsummer, Mikael J. http://www.iki.fi/~mpjohans/ On Thu, 23 Jun 2011, Sergio Emanuel Galembeck segalemb~~usp.br wrote: > > Sent to CCL by: Sergio Emanuel Galembeck [segalemb*_*usp.br] > > Dear Mico, > > The location of the extra electron could be found in the spin > density matrix, or density of alpha minus beta electrons. > To calculate a radical anion you need to specify charge = -1 > and multiplicity = 2. > > Best regards, > > Sergio > > Citando "Mico Leggesse ermiaslegg{}gmail.com" : > >> >> Sent to CCL by: "Mico Leggesse" [ermiaslegg,gmail.com] >> Dear All; >> Can any one tell me how i could locate the additional electron in the >> radical >> anion using Gaussian 09 package? also could you tell me how i should >> proceed if >> i want to study the addition of one electron to this radical anion? >> Thank You in advance!http://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/> From owner-chemistry@ccl.net Thu Jun 23 15:52:00 2011 From: "Adam C Sykes adam.sykes---quanano.co.uk" To: CCL Subject: CCL: Using AMD APP for computational chemistry & EVGA SR-2 motherboard Message-Id: <-44968-110623155033-8253-uYbbINyfkHbuVuB4TN8kjg::server.ccl.net> X-Original-From: "Adam C Sykes" Date: Thu, 23 Jun 2011 15:50:31 -0400 Sent to CCL by: "Adam C Sykes" [adam.sykes-.-quanano.co.uk] Dear All, I am wondering about the current state of software available for quantum mechanics and molecular mechanics/dynamics, that makes use of AMDs APP and therefore, AMD/ATI GPUs. I am considering building a system based on the Dual Xeon EVGA SR-2 motherboard, which would support multiple AMD Radeon HD 6990 cards. Does anyone have any experience of using AMD GPUs, rather than Nvidia with CUDA? Thanks, Adam From owner-chemistry@ccl.net Thu Jun 23 16:51:01 2011 From: "Sherin Alfalah shireenfalah^-^hotmail.com" To: CCL Subject: CCL: more on "starting point to read/learn docking" Message-Id: <-44969-110623143230-11209-U+L6roEC82/sKdPLiVVS/Q a server.ccl.net> X-Original-From: "Sherin Alfalah" Date: Thu, 23 Jun 2011 14:32:26 -0400 Sent to CCL by: "Sherin Alfalah" [shireenfalah\a/hotmail.com] Dear CCL users, Dear Karen, Thanks a lot for your advice. To clarify more, I have not done any docking calculations before. I am a quantum chemist, I have carried out quantum chemistry calculations, quantum dynamics calculations but no docking. Also I have perfomed some QSAR calculations. The tutorials of the docking programs explain how to run the calculations but one has to chose some parameters which requires understanding the theory. Also, how can I know that my calculations are OK or meaningless! All of this require knowing the very basic/initial theory which I do not know but I would like to learn! Any suggestions to start from would be highly appreciated. Thanks in advance Best wishes Sherin Alfalah > Subject: RE: starting point to read/learn docking > Date: Thu, 23 Jun 2011 10:47:57 -0700 > From: Karen.Green(-)sanofi-aventis.com > To: shireenfalah(-)hotmail.com > > Dear Sherin, > > If you could explain a little more about what type of calculations you > have done in the past and why the current papers are too advanced, you > might get responses better tailored to your background. > > Karen > > > > Sent to CCL by: "Sherin Alfalah" [shireenfalah===hotmail.com] Dear CCL > people, I am a computational chemist who wants to learn docking. There > are some free software packages with good tutorials but I am wondering > which book, reviews, articles can help as starting point to read about > (or learn) the theory of docking? > All the material I managed to find are "advanced" while I would > appreciate any recommendations for more "basic" material. > Thanks in advance > Best regards > Sherin Alfalah From owner-chemistry@ccl.net Thu Jun 23 17:26:00 2011 From: "Wilfred W Li wilfred : ucsd.edu" To: CCL Subject: CCL: NBCR Summer Institute 2011 Message-Id: <-44970-110623154935-7736-9v+5YtMolmYuGpjNeV044w[A]server.ccl.net> X-Original-From: "Wilfred W Li" Date: Thu, 23 Jun 2011 15:49:33 -0400 Sent to CCL by: "Wilfred W Li" [wilfred,+,ucsd.edu] The National Biomedical Computation Resource (NBCR) will hold its 6th Summer Institute (SI) August 1-5, 2011, in La Jolla California, on the UC San Diego campus. http://si.nbcr.net. Highlights of What's New for SI 2011: Computational Cardiac Mechanics: Continuity 6.4beta was released on April 12, 2011, with improved Biomechanics module, a new database for model sharing and GPU computing support. Mesoscale Modeling of Cardiac Myocytes: Newly released GAMer and CSMOL interface through Blender for mesh refinement, and simulation of subcellular calcium dynamics using realistic geometry in cardiac muscle cells. Molecular Electrostatics and Diffusion: Improved APBS and PDB2PQR for electrostatic calculations, and BrownDye for Brownian Dynamics of biological molecules. Virtual Screening using AutoDock Suite of Tools: New AutoDock 4.2.3 and AutoDock Vina improvements, especially new features that facilitate postanalysis using AutoDockTools, PyRx, and Raccoon. Computer Aided Drug Discovery (CADD) pipeline: Pipelines built from commonly used workflows in CADD, with a focus on the Relaxed Complex Scheme (RCS) for capturing the dynamic nature of protein conformations. Scalable Scientific Applications and Workflows using Cloud Services: Programming scalable scientific applications using GPU and making your own application accessible in the Cloud computing environment. Registration Opens:May 14, 2011 Scholarship Application deadline:June 25, 2011 Scholarship decision announced:July 8, 2011 Campus Housing and meals deadline:July 18, 2011 Registration Closes:July 29, 2011 Flyer: http://www.nbcr.net/si/2011/NBCR_2011_SI.pdf Background: NBCR SI aims to provide significant training opportunities for members of the biomedical research community in targeted areas of computational multiscale biomedical research: computer aided drug discovery; mesoscale modeling; and computational cardiac electrophysiology and mechanics. Training will include hands-on use of key NBCR tools that are freely available to the academic community. There will be opportunities for participants to work with their own data and analyses in extended sessions. This years workshop will have three major activities: 1. In-depth, Hands-on Training sessions in key areas of multiscale biomedical research; 2. Plenary Talks on multiscale computational modeling; 3. Special Sessions, including special short topics or additional time with instructors to work with student brought data. In addition to training, students will be able to hear talks on new directions under the theme of multiscale computational modeling. There will also be a poster session to allow NBCR instructors and researchers to interact with the participants and explore new opportunities for collaboration or user needs. Please forward to colleagues who may be interested. From owner-chemistry@ccl.net Thu Jun 23 18:01:00 2011 From: "Robert Perkins cclnanolab()gmail.com" To: CCL Subject: CCL: g09 on stallo Message-Id: <-44971-110623133241-24107-JIdpgD4bppdQ1eQhLJj+kA|*|server.ccl.net> X-Original-From: Robert Perkins Content-Type: multipart/alternative; boundary=000e0cd290f86315b104a6647876 Date: Thu, 23 Jun 2011 19:32:33 +0200 MIME-Version: 1.0 Sent to CCL by: Robert Perkins [cclnanolab a gmail.com] --000e0cd290f86315b104a6647876 Content-Type: text/plain; charset=ISO-8859-1 Hi, Could anyone please send me a sample script file to run g09 jobs on stallo? Thank you in advance. RP --000e0cd290f86315b104a6647876 Content-Type: text/html; charset=ISO-8859-1 Hi,
Could anyone please send me a sample script file to run g09 jobs on stallo?
Thank you in advance.
RP
--000e0cd290f86315b104a6647876-- From owner-chemistry@ccl.net Thu Jun 23 18:35:01 2011 From: "Cen Gao cengao:_:gmail.com" To: CCL Subject: CCL: more on "starting point to read/learn docking" Message-Id: <-44972-110623174715-21624-om6U+3TMoL0jyI7yPy4jfg()server.ccl.net> X-Original-From: Cen Gao Content-Type: multipart/alternative; boundary=90e6ba615388a81b1704a6680605 Date: Thu, 23 Jun 2011 17:47:05 -0400 MIME-Version: 1.0 Sent to CCL by: Cen Gao [cengao|gmail.com] --90e6ba615388a81b1704a6680605 Content-Type: text/plain; charset=ISO-8859-1 Hi Sherin: The following reviews and their references might be of your interest. Kitchen, D. B., Decornez, H., Furr, J. R., & Bajorath, J. (2004). Docking and scoring in virtual screening for drug discovery: methods and applications. *Nature reviews. Drug discovery*, *3*(11), 935-49. doi: 10.1038/nrd1549. Brooijmans, N., & Kuntz, I. D. (2003). Molecular recognition and docking algorithms. *Annual review of biophysics and biomolecular structure*, *32*, 335-73. doi: 10.1146/annurev.biophys.32.110601.142532. Best, Cen On Thu, Jun 23, 2011 at 2:32 PM, Sherin Alfalah shireenfalah^-^hotmail.com < owner-chemistry*_*ccl.net> wrote: > > Sent to CCL by: "Sherin Alfalah" [shireenfalah\a/hotmail.com] > Dear CCL users, > Dear Karen, Thanks a lot for your advice. > To clarify more, I have not done any docking calculations before. > I am a quantum chemist, I have carried out quantum chemistry calculations, > quantum dynamics calculations but no docking. Also I have perfomed some QSAR > calculations. > The tutorials of the docking programs explain how to run the calculations > but one has to chose some parameters which requires understanding the > theory. > Also, how can I know that my calculations are OK or meaningless! > All of this require knowing the very basic/initial theory which I do not > know but I would like to learn! > Any suggestions to start from would be highly appreciated. > Thanks in advance > Best wishes > Sherin Alfalah > > > > Subject: RE: starting point to read/learn docking > > Date: Thu, 23 Jun 2011 10:47:57 -0700 > > From: Karen.Green##sanofi-aventis.com > > To: shireenfalah##hotmail.com > > > > Dear Sherin, > > > > If you could explain a little more about what type of calculations you > > have done in the past and why the current papers are too advanced, you > > might get responses better tailored to your background. > > > > Karen > > > > > > > > Sent to CCL by: "Sherin Alfalah" [shireenfalah===hotmail.com] Dear CCL > > people, I am a computational chemist who wants to learn docking. There > > are some free software packages with good tutorials but I am wondering > > which book, reviews, articles can help as starting point to read about > > (or learn) the theory of docking? > > All the material I managed to find are "advanced" while I would > > appreciate any recommendations for more "basic" material. > > Thanks in advance > > Best regards > > Sherin Alfalah> > > --90e6ba615388a81b1704a6680605 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Hi Sherin:

T= he following reviews and their references might be of your interest.

Kitchen, D. B., Decornez, H., Furr, J. R., & Bajorath, J. (2004).=20 Docking and scoring in virtual screening for drug discovery: methods and applications. Nature reviews. Drug discovery, 3(11), 935-49.= doi: 10.1038/nrd1549.

=A0=A0=A0=A0=A0=A0=A0 Brooijmans, N., & Kuntz, I. D. (2003). Molecular= recognition and docking algorithms. Annual review of biophysics and bio= molecular structure, 32, 335-73. doi: 10.1146/annurev.biophys.32= .110601.142532.


Bes= t,

Cen




On Thu, Jun 23, 2011 at 2:32 PM, Sheri= n Alfalah shireenfalah^-^hotmail.com <owner-chemist= ry*_*ccl.net> wrote:

Sent to CCL by: "Sherin =A0Alfalah" [shireenfalah\a/hotmail.com]
Dear CCL users,
Dear Karen, Thanks a lot for your advice.
To clarify more, I have not done any docking calculations before.
I am a quantum chemist, I have carried out quantum chemistry calculations, = quantum dynamics calculations but no docking. Also I have perfomed some QSA= R calculations.
The tutorials of the docking programs explain how to run the calculations b= ut one has to chose some parameters which requires understanding the theory= .
Also, how can I know that my calculations are OK or meaningless!
All of this require knowing the very basic/initial theory which I do not kn= ow but I would like to learn!
Any suggestions to start from would be highly appreciated.
Thanks in advance
Best wishes
Sherin Alfalah


> Subject: RE: starting point to read/learn docking
> Date: Thu, 23 Jun 2011 10:47:57 -0700
> From: Karen.Green##sanofi-aventis.com
> To: shireenfalah##hot= mail.com
>
> Dear Sherin,
>
> If you could explain a little more about what type of calculations you=
> have done in the past and why the current papers are too advanced, you=
> might get responses better tailored to your background.
>
> Karen
>
>
>
> Sent to CCL by: "Sherin Alfalah" [shireenfalah=3D=3D=3Dhotmail.com] Dear CCL
> people, I am a computational chemist who wants to learn docking. There=
> are some free software packages with good tutorials but I am wondering=
> which book, reviews, articles can help as starting point to read about=
> (or learn) the theory of docking?
> All the material I managed to find are "advanced" while I wo= uld
> appreciate any recommendations for more "basic" material. > Thanks in advance
> Best regards
> Sherin Alfalah



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