From owner-chemistry@ccl.net Thu Jan 19 00:44:00 2012 From: "Neese, Frank frank.neese.:.mpi-mail.mpg.de" To: CCL Subject: CCL: G09: CCSD method and large basis Sets Message-Id: <-46164-120119004102-21088-jzH79cVQA0NPlqKILvnLjA/./server.ccl.net> X-Original-From: "Neese, Frank" Content-Language: de-DE Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Thu, 19 Jan 2012 06:43:39 +0100 MIME-Version: 1.0 Sent to CCL by: "Neese, Frank" [frank.neese#mpi-mail.mpg.de] Dear Roger, I guess that Orca could do the coupled cluster calculations that you mentioned. You find for free at http://www.mpibac.mpg.de/bac/index_en.php in the download area. All the best, Frank Am 18.01.2012 um 20:30 schrieb "Sebastian Kozuch kozuchs-,-yahoo.com" >: A good compromise between accuracy and timing is achieved with double hybrid DFT. Usually much more accurate than hybrid functionals, and for sure much faster than couple cluster. However, if you need chemical accuracy (~1 kcal/mol) you should first compare them to CCSD(T)/CBS with a small model system. And always pray that you don't have big non-dynamic correlation, or even couple cluster will be a failure! xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ..........Sebastian Kozuch........... xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ....Weizmann Institute of Science.... ...........Rehovot, Israel........... .. sebastian.kozuch()weizmann.ac.il .. http://yfaat.ch.huji.ac.il/kozuch.htm xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx ________________________________ > From: Roger Robinson scu98rkr%a%gmail.com > To: "Kozuch, Sebastian " > Sent: Wednesday, January 18, 2012 6:05 PM Subject: CCL: G09: CCSD method and large basis Sets Sent to CCL by: Roger Robinson [scu98rkr^-^gmail.com] Dear All, I want to accurately calculate barrier heights for several sets of reactions. I am looking at molecules up to say 9-10 large atoms + Hydrogens. Currently I am using G09 for my calculations For most of my work I am looking at using the M06-2X functional for calculating geometries, frequencies and zero point energies and for other bits and bobs. I have just about managed to install GAMESS and I am considering maybe the M08-SO functional for future work. But a I also need to calculate the barrier heights with as much precision as possible. I have looked at a few papers such as Kinetics of hydrogen-transfer isomerizations of butoxyl radicals by Zhen and Truhlar They suggest CCSD(T)/CBS+CV+Rel.//M06-2X/MG3S as a very accurate method. Im looking at slightly bigger molecules them and I probably dont have the same resources available as them. I have managed to calculate barrier heights at the CCSD(T)/aug-cc-pVDZ//M06-2X/MG3S level so far. I am currently trying to do so at the CCSD(T)/aug-cc-pVTZ//M06-2X/MG3S level. So far the RWF files have got to ~330GB ! Im not too sure I have the resources to do this. The Timings Comparisons on http://cccbdb.nist.gov/ Seem to suggest VTZ will be 42 slower for a molecule with 3 large atoms, which does nt sound right to me. This might be becuase the examples on http://cccbdb.nist.gov/ run quite quickly so there is alot of I/O activity ? 42 times longer would be well beyond my capabilities. Does anyone have any though on CCSD(T)/maug-cc-pVTZ or CCSD(T)/cc-VTZ. Would CCSD(T)/aug-cc-pVDZ//M06-2X/MG3S be about as accurate as Im going to get for a molecule with 9 carbons ? I can use 12 core machine shared memory machines but Im hoping the jobs last weeks not months. Any help appreciated, Rogerthe 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 usehttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Jan 19 08:37:00 2012 From: "Senthil kumar Krishnasamy supersenthil73~!~rediffmail.com" To: CCL Subject: CCL: Error termination of the job & unit of spin density Message-Id: <-46165-120119033416-19387-AYvsoL/LYXZJFtwM9modyA()server.ccl.net> X-Original-From: "Senthil kumar Krishnasamy" Date: Thu, 19 Jan 2012 03:34:15 -0500 Sent to CCL by: "Senthil kumar Krishnasamy" [supersenthil73 a rediffmail.com] Dear all Pl clarify my two doubts as stated below (i) I have the following error during the freq calculation of quercetin radical at PM3 method with the following route section # PM3 Freq SE2nd: IAtom= 5 IXYZ=2 IS=2. SE2nd: IAtom= 5 IXYZ=3 IS=1. SE2nd: IAtom= 5 IXYZ=3 IS=2. SE2nd: IAtom= 6 IXYZ=1 IS=1. SE2nd: IAtom= 6 IXYZ=1 IS=2. SE2nd: IAtom= 6 IXYZ=2 IS=1. SE2nd: IAtom= 6 IXYZ=2 IS=2. SE2nd: IAtom= 6 IXYZ=3 IS=1. SE2nd: IAtom= 6 IXYZ=3 IS=2. SE2nd: IAtom= 7 IXYZ=1 IS=1. SE2nd: IAtom= 7 IXYZ=1 IS=2. SE2nd: IAtom= 7 IXYZ=2 IS=1. SE2nd: IAtom= 7 IXYZ=2 IS=2. SE2nd: IAtom= 7 IXYZ=3 IS=1. SE2nd: IAtom= 7 IXYZ=3 IS=2. SE2nd: IAtom= 8 IXYZ=1 IS=1. SE2nd: IAtom= 8 IXYZ=1 IS=2. SE2nd: IAtom= 8 IXYZ=2 IS=1. SE2nd: IAtom= 8 IXYZ=2 IS=2. SE2nd: IAtom= 8 IXYZ=3 IS=1. SE2nd: IAtom= 8 IXYZ=3 IS=2. SE2nd: IAtom= 9 IXYZ=1 IS=1. SE2nd: IAtom= 9 IXYZ=1 IS=2. SE2nd: IAtom= 9 IXYZ=2 IS=1. ALL CONVERGERS ARE NOW FORCED ON SHIFT=1000, PULAY ON, CAMP-KING ON AND ITERATION COUNTER RESET """""""""""""UNABLE TO ACHIEVE SELF-CONSISTENCE DELTAE= 0.1173E+05 DELTAP= 0.2361E-01 (ii) What is the unit of atomic spin densities located on each atom on phenyl ring at the single point energy calculation? Thanks in advance By K. Senthil kumar Faculty of Physics Hindusthan college of engg & tech Coimbatore-32 India From owner-chemistry@ccl.net Thu Jan 19 09:37:00 2012 From: "Tamas Gunda tgunda2 . puma.unideb.hu" To: CCL Subject: CCL: Chemical Drawing Programs review Message-Id: <-46166-120119093421-29206-/XeYFym9AjsF9J61hPrS8A,server.ccl.net> X-Original-From: "Tamas Gunda" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-2"; reply-type=original Date: Thu, 19 Jan 2012 15:34:52 +0100 MIME-Version: 1.0 Sent to CCL by: "Tamas Gunda" [tgunda2-.-puma.unideb.hu] Dear CCL members, A major upgrade of my e-review on chemical drawing programs was performed. ChemDoodle has been added, MarvinSketch has also been discussed in detail, and several small applications have been added and dead projects have been removed, etc. If you are interested have a look at: http://dragon.unideb.hu/~gundat/rajzprogramok/dprog.html Tamas Gunda From owner-chemistry@ccl.net Thu Jan 19 10:34:00 2012 From: "Wolf Ihlenfeldt wdi/a\xemistry.com" To: CCL Subject: CCL: Chemical Drawing Programs review Message-Id: <-46167-120119102624-16860-DwQaxMTwncMsBh9JRKJ74Q,+,server.ccl.net> X-Original-From: Wolf Ihlenfeldt Content-Type: multipart/alternative; boundary=bcaec51b175f58b81004b6e32f3d Date: Thu, 19 Jan 2012 16:26:14 +0100 MIME-Version: 1.0 Sent to CCL by: Wolf Ihlenfeldt [wdi===xemistry.com] --bcaec51b175f58b81004b6e32f3d Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Strangely, this review is completely missing the technologically unique Web sketcher originally developed for PubChem and accessible in an enhanced version at www.xemistry.com/edit/frame.html This tool is the only full-featured Web structure editor which is *not* a plug-in (with all its platform and installation issues) nor a Java applet (with its own JVM engine presence and versioning problems, plus download time issues). Compared to other Web editors of any kind, it can access a much broader range of Internet structure databases directly (over 2 dozen currently), and it supports a much larger list of I/O formats (for example, it supports SDF3000 and original ChemDraw CDX/CDXML or ISISDraw skc/tgf files as well as direct input and decoding of SMILES, SLN, JME strings, PubChem CIDs, cas numbers, compound names, etc.). On Thu, Jan 19, 2012 at 3:34 PM, Tamas Gunda tgunda2 . puma.unideb.hu < owner-chemistry^_^ccl.net> wrote: > > Sent to CCL by: "Tamas Gunda" [tgunda2-.-puma.unideb.hu] > Dear CCL members, > > A major upgrade of my e-review on chemical drawing programs was performe= d. > ChemDoodle has been added, MarvinSketch has also been discussed in detail= , > and several small applications have been added and dead projects have bee= n > removed, etc. > If you are interested have a look at: > > http://dragon.unideb.hu/~**gundat/rajzprogramok/dprog.**html > > Tamas Gunda > > > > -=3D This is automatically added to each message by the mailing script = =3D-> http://www.ccl.net/cgi-bin/**ccl/send_ccl_message http://www.ccl.net/cgi-bin/**ccl/send_ccl_message chemistry/announcements/**conferences/ > > Search Messages: http://www.ccl.net/chemistry/**searchccl/index.shtml http://www.ccl.net/spammers.**txt > > RTFI: http://www.ccl.net/chemistry/**aboutccl/instructions/ > > > --=20 Wolf-D. Ihlenfeldt - Xemistry GmbH - wdi^_^xemistry.com Phone: +49 6174 201455 - Fax +49 6174 209665 --- xemistry gmbh =E2=80=93 Gesch=C3=A4ftsf=C3=BChrer/Managing Director: Dr. W.= D. Ihlenfeldt Address: Hainholzweg 11, D-61462 K=C3=B6nigstein, Germany HR K=C3=B6nigstein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719 --bcaec51b175f58b81004b6e32f3d Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Strangely, this review is completely missing the technologically unique= Web sketcher originally developed for PubChem and accessible in an enhance= d version at www.xemist= ry.com/edit/frame.html

This tool is the only full-featured Web structure editor which is *not*= a plug-in (with all its platform and installation issues) nor a Java apple= t (with its own JVM engine presence and versioning problems, plus download = time issues). Compared to other Web editors of any kind, it can=C2=A0 acces= s a much broader range of Internet structure databases directly (over 2 doz= en currently), and it supports a much larger list of I/O formats (for examp= le, it supports SDF3000 and original ChemDraw CDX/CDXML or ISISDraw skc/tgf= files as well as direct input and decoding of SMILES, SLN, JME strings, Pu= bChem CIDs, cas numbers, compound names, etc.).

On Thu, Jan 19, 2012 at 3:34 PM, Tamas Gunda= tgunda2 . puma.unideb.hu <owner-chemistry^_^ccl= .net> wrote:

Sent to CCL by: "Tamas Gunda" [tgunda2-.-puma.unideb.hu]
Dear CCL members,

A major upgrade of my =C2=A0e-review on chemical drawing programs was perfo= rmed.
ChemDoodle has been added, MarvinSketch has also been discussed in detail,<= br> and several small applications have been added and dead projects have been = removed, etc.
If you are interested have a look at:

http://dragon.unideb.hu/~gundat/rajzprogramok/dprog.html

Tamas Gunda



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

E-mail to administrators: CHEMISTRY-REQUEST^_^ccl.net or use
=C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/chemistry/= sub_unsub.shtml

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

Job: http://www.ccl.n= et/jobs Conferences: http://server.ccl.net/chemist= ry/announcements/conferences/

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

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





--
Wolf-D. Ihlenfeldt -=C2= =A0 Xemistry GmbH - w= di^_^xemistry.com
Phone: +49 6174 201455 - Fax +49 6174 209665
---<= br>xemistry gmbh =E2=80=93 Gesch=C3=A4ftsf=C3=BChrer/Managing Director: Dr.= W. D. Ihlenfeldt
Address: Hainholzweg 11, D-61462 K=C3=B6nigstein, Germany
HR K=C3=B6nigs= tein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719

--bcaec51b175f58b81004b6e32f3d-- From owner-chemistry@ccl.net Thu Jan 19 11:09:00 2012 From: "Jose R. Valverde jrvalverde++cnb.csic.es" To: CCL Subject: CCL: 8-oxo-GTP Message-Id: <-46168-120119051647-23469-UQ/zrgf6ibNKe8gs//Olfg(0)server.ccl.net> X-Original-From: "Jose R. Valverde" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Thu, 19 Jan 2012 11:16:15 +0100 Mime-Version: 1.0 Sent to CCL by: "Jose R. Valverde" [jrvalverde%%cnb.csic.es] Hi Ed, thanks. I had assumed all reported structures would be at physiological pH, but now you mention it, it is possible the protonation state may change on the receptor moiety thus yielding different structures which would explain them. Silly me. j On Mon, 16 Jan 2012 10:55:39 +0000 "Edward Holland hollandej]_[Cardiff.ac.uk" wrote: > > Sent to CCL by: Edward Holland [hollandej%a%Cardiff.ac.uk] > Hi Jose, > > The protonation state of molecules can depend on the pH of the environment they are in. You should be able to work out what you require from pKa data. > > Yours > > Ed Holland > > On 16 Jan 2012, at 10:03, Jose R. Valverde jrvalverde^cnb.csic.es wrote: > > > > > Sent to CCL by: "Jose R. Valverde" [jrvalverde+/-cnb.csic.es] > > Hi all, > > > > I am interested in the structure of 8-oxo-GTP to run some calculations, > > but I am having a hard time deciding which is its structure. A cursory look in > > Google reveals several different structures all under the same name, viz: > > > > PDBeChem > > http://www.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/8GT > > > > ChEBI > > http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=1wuq&template=ligands.html&l=1.1 > > (this one seems to lack the H, but might be valid with appropriate double > > bonds) > > > > Jena Bioscience > > http://www.jenabioscience.com/images/2d0798249a/NU-1116.pdf > > (this one puts the H on the O) > > > > Chemical Book > > http://www.chemicalbook.com/ProductChemicalPropertiesCB6780463_EN.htm > > This adds the H on a different N > > > > PubChem > > http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=167974 > > This puts two H on different places as well > > > > > > The problem is you can find references using any of them and calling it the > > same, so any of them might be valid, but depending on where H are, the H-bonding > > network on union to an enzyme would change. So, which is/should be it? Does it > > make any difference? Any suggestion? > > > > Of course I understand that for X-ray structure determination of complexes it > > makes no difference as H are normally not detected nor reported, but in order > > to understand the interaction mechanisms the choice might have an impact. > > > > Thanks. > > j > > -- > > EMBnet/CNB > > Scientific Computing Service > > Solving all your computer needs for Scientific > > Research. > > > > http://bioportal.cnb.csic.es > > http://www.es.embnet.org> > -- EMBnet/CNB Scientific Computing Service Solving all your computer needs for Scientific Research. http://bioportal.cnb.csic.es http://www.es.embnet.org From owner-chemistry@ccl.net Thu Jan 19 13:22:00 2012 From: "Harald Lanig harald.lanig++chemie.uni-erlangen.de" To: CCL Subject: CCL: Molecular Modelling Workshop 2012 in Erlangen, Germany Message-Id: <-46169-120119103827-4188-Ar+5wkegaBH8qwMO+FLgoA%server.ccl.net> X-Original-From: Harald Lanig Content-Disposition: inline Content-Type: text/plain; charset="US-ASCII"; format="flowed" Date: Thu, 19 Jan 2012 16:37:28 +0100 MIME-Version: 1.0 Sent to CCL by: Harald Lanig [harald.lanig*_*chemie.uni-erlangen.de] Dear list subscribers, this year, the traditional Molecular Modelling Workshop in Erlangen (formerly known as "Darmstadt workshop") takes place on March, Monday 12th to Wednesday 14th, 2012. Starting on Monday after lunch should allow to avoid travelling on weekend keeping the expenses at a minimum. ####### Plenary Speakers ####### We are very happy to announce that two leading experts in their field have agreed to give a plenary talk at the meeting: Prof. Peter Comba University of Heidelberg Prof. Francesco Gervasio Spanish National Cancer Research Center ####### Bursaries available ####### There are a limited number of MGMS-DS travel bursaries for students available upon request. Please apply for all support to mmws[*]mgms-ds.de ####### Poster and Lecture Awards ####### As in the past years, there will be two Poster Awards of EUR 100,-- each and three Lecture Awards for the best talks: 1st Winner: Travel bursary to the Young Modellers Forum in the United Kingdom (travel expenses are reimbursed up to EUR 500) 2nd Winner: EUR 200,-- travel expenses reimbursement 3rd Winner: EUR 100,-- travel expenses reimbursement Only undergraduate and graduate research students qualify for the poster and lecture awards. As every year, an interesting and successful workshop depends on your contributions. Therefore let me invite you to submit talks and/or poster titles via the registration form accessible on the workshop Web site http://www.chemie.uni-erlangen.de/ccc/conference/mmws12/ This Web site will provide all necessary information about the meeting! The deadline for all submissions is February 24th, 2012. I am looking forward to meeting you in Erlangen soon! -Harald Lanig -- ------------------------------------------------------------------------ Dr. Harald Lanig Universitaet Erlangen/Nuernberg Computer-Chemie-Centrum Naegelsbachstr. 25, D-91052 Erlangen Phone +49(0)9131-85 26525 harald DOT lanig AT chemie.uni-erlangen.de Fax +49(0)9131-85 26565 http://www.chemie.uni-erlangen.de/lanig ------------------------------------------------------------------------ From owner-chemistry@ccl.net Thu Jan 19 18:09:00 2012 From: "Arne Dieckmann adieckma(-)googlemail.com" To: CCL Subject: CCL:G: Low frequencies Message-Id: <-46170-120119180817-20212-av8WFMVL7/HM2T0v22/sZA-$-server.ccl.net> X-Original-From: Arne Dieckmann Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Thu, 19 Jan 2012 15:08:10 -0800 Mime-Version: 1.0 (Apple Message framework v1251.1) Sent to CCL by: Arne Dieckmann [adieckma#,#googlemail.com] Dear all, I am optimizing a series of quite large molecules (102 atoms, more than half of those are C,N,O) using the M062X functional. A closer look at the calculated frequencies reveals that 80 of 300 vibrations are below Gaussian's threshold of 625 cm^-1 for "low frequencies". I have repeated the frequency calculation using the HinderedRotor option, which produced exactly the same values for thermal corrections, although 26 vibrations were identified as really being rotations. In another calculation on the same system, I substracted the contribution of those 80 vibrations using the freqchk utility resulting in substantially different values for thermal corrections. Would you consider those values to be more reliable than the initial ones? Best regards, Arne - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Dr. Arne Dieckmann Houk Research Lab | University of California, Los Angeles From owner-chemistry@ccl.net Thu Jan 19 22:58:01 2012 From: "Gonzalo Jimenez Oses gjimenez**chem.ucla.edu" To: CCL Subject: CCL:G: Low frequencies Message-Id: <-46171-120119203249-26369-/CNABjWP+3T+vqJhpMnUOQ#%#server.ccl.net> X-Original-From: "Gonzalo Jimenez Oses" Date: Thu, 19 Jan 2012 20:32:38 -0500 Sent to CCL by: "Gonzalo Jimenez Oses" [gjimenez[*]chem.ucla.edu] Dear Arne, Well, the problem is that, if I'm not wrong, you always need 3N-6 vibrations in the ground state (3N-7 in the TS) for the vibrational/thermal analysis to make sense. I guess you cannot simple get rid of an arbitrary number of vibrations. This is the price you need to pay when calculating frequencies of big and flexible molecules. More sophisticated methods to accurately describe thermal/entropic contributions would involve dynamics, which, of course is unfeasible at QM levels for most of our systems. I've wrote a silly program to calculate the partition functions with any nunmber of the calculated frequencies (overriding theory!), and I could experience in my bones that the smallest frequencies contribute the most to the thermal/entropic corrections. This means that you'll always have errors when comparing related structures when moving from DeltaH to DeltaG, which, yes, it's really annoying. I guess that there is not a rule of thumb for this. Small (and not so small) frequencies appear here and there, depending on the method (m06-2x in gaussian is painful), solvent method, grid size, convergence criteria... This is why DeltaG are so unrealistic when dealing with big molecules (but, yeah, usually our bosses and referees want them, don't they?) Best, Gonzalo -------------------------------------------------- > From: "Arne Dieckmann adieckma(-)googlemail.com" Sent: Thursday, January 19, 2012 3:08 PM To: "Oses, Gonzalo Jimenez " Subject: CCL:G: Low frequencies > > Sent to CCL by: Arne Dieckmann [adieckma#,#googlemail.com] > Dear all, > > I am optimizing a series of quite large molecules (102 atoms, more than > half of those are C,N,O) using the M062X functional. A closer look at the > calculated frequencies reveals that 80 of 300 vibrations are below > Gaussian's threshold of 625 cm^-1 for "low frequencies". I have repeated > the frequency calculation using the HinderedRotor option, which produced > exactly the same values for thermal corrections, although 26 vibrations > were identified as really being rotations. In another calculation on the > same system, I substracted the contribution of those 80 vibrations using > the freqchk utility resulting in substantially different values for > thermal corrections. Would you consider those values to be more reliable > than the initial ones? > > > Best regards, > Arne > > - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - > - - - - - - - - - - - - > Dr. Arne Dieckmann > Houk Research Lab | University of California, Los Angeles> >