From owner-chemistry@ccl.net Tue Mar 4 00:11:01 2008 From: "carlos simmerling carlos.simmerling.:.stonybrook.edu" To: CCL Subject: CCL: Final call for ACS/CCG graduate student research excellence awards Message-Id: <-36397-080303190329-26063-lEEf4VG45CD/Bb+ZIspXYQ=-=server.ccl.net> X-Original-From: "carlos simmerling" Date: Mon, 3 Mar 2008 19:03:26 -0500 Sent to CCL by: "carlos simmerling" [carlos.simmerling^^^stonybrook.edu] Please note that the deadline is this week! Share this information with any graduate student. Note that eligible students can reside in North, Central or South America. 5 $1,150 CCG Excellence Student Travel Award Stipends Available for the Fall 2008 Philadelphia ACS National Meeting The CCG Excellence Awards have been created to stimulate graduate student participation in ACS COMP Division activities (symposia and poster sessions) at ACS National Meetings. Those eligible for a CCG Excellence Award are graduate students, working in the Americas, that are in good standing and will present work within the COMP program, either in oral or poster format. Winners receive $1,150, as well as a copy of CCG's MOE (Molecular Operating Environment) software with a one-year license. They are also honored during a ceremony at the COMP Division Poster Session. The application consists of an extended abstract (no more than 2 pages) of the poster or presentation along with a letter of support from the research advisor, a two page CV, and a personal statement (no more than 1 page). The awardees are chosen on the basis of the quality and significance of the research to be presented, as well as the strength of the supporting letter and other materials. All graduate students of the Americas are encouraged to submit applications. Awards will be given only to those individuals making presentations, not co-authors. Closing date for entries (including all required supporting info.) is Friday, March 7, 2008 at 5PM Eastern time. Note that the award application deadline is BEFORE the normal deadline for submission of abstracts for the meeting. Applicants will receive email confirmation of receipt of materials. If you do not receive confirmation by March 10, 2008, please contact the organizer immediately by telephone (see below). In addition, you must submit your normal abstract to the " Chemical Computing Group Excellence Award" symposium on the OASYS system (the COMP OASYS deadline is March 17, 2008 for the Philadelphia ACS Meeting) More information on awards offered by the ACS COMP division can be found on the web site at http://membership.acs.org/c/Comp/awards.html Carlos Simmerling Chair, ACS COMP Division Awards Committee Professor, Department of Chemistry Stony Brook University Stony Brook, NY 11794-3400 631-384-9248 carlos.simmerling : gmail.com From owner-chemistry@ccl.net Tue Mar 4 00:46:00 2008 From: "Dibyadeep Paul dibyadeep:+:gmail.com" To: CCL Subject: CCL: GROMACS vs NAMD Message-Id: <-36398-080303195525-1761-fNepvFDDrYlCO3lYNImSxg ~ server.ccl.net> X-Original-From: "Dibyadeep Paul" Content-Type: multipart/alternative; boundary="----=_Part_9972_32282331.1204588455429" Date: Tue, 4 Mar 2008 05:24:15 +0530 MIME-Version: 1.0 Sent to CCL by: "Dibyadeep Paul" [dibyadeep_._gmail.com] ------=_Part_9972_32282331.1204588455429 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hii... Could somebody kindly point out to me the essential difference between the simulation procedures between NAMD and GROMACS. I am familiar with NAMD, but since I am running it on a single processor machine I hear that GROMACS would be much more efficient. Is there any comparison of the results available on publicly available literature. If so it would be very kind if somebody knowledgeable could kindly point that out to me, or send me the relevent paper. Sincerely Dibyadeep ------=_Part_9972_32282331.1204588455429 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hii...

Could somebody kindly point out to me the essential difference between the simulation procedures between NAMD and GROMACS. I am familiar with NAMD, but since I am running it on a single processor machine I hear that GROMACS would be much more efficient. Is there any comparison of the results available on publicly available literature. If so it would be very kind if somebody knowledgeable could kindly point that out to me, or send me the relevent paper.

Sincerely

Dibyadeep
------=_Part_9972_32282331.1204588455429-- From owner-chemistry@ccl.net Tue Mar 4 01:24:00 2008 From: "carlos simmerling carlos.simmerling:+:stonybrook.edu" To: CCL Subject: CCL: Final call for ACS/HP Junior Faculty Award Applications Message-Id: <-36399-080303185911-25532-8+4vcRJZBkwaSgsIpMiJ2Q]*[server.ccl.net> X-Original-From: "carlos simmerling" Date: Mon, 3 Mar 2008 18:59:07 -0500 Sent to CCL by: "carlos simmerling" [carlos.simmerling===stonybrook.edu] Please note that the deadline for applications for the award is this week! Please spread the word throughout the community and encourage junior faculty to apply. Postdocs in transition to faculty positions are also eligible. The HP Outstanding Junior Faculty Award program provides $1,000 to each of four outstanding tenure-track junior faculty members to present their work in COMP symposia at ACS National Meetings. The Awards are designed to assist new faculty members in gaining visibility within the COMP community. Award certificates and $1,000 prizes will be presented at the COMP Poster session. While special consideration will be given to Assistant Professors presenting work in the area of algorithm and methods development, applications for HP Outstanding Junior Faculty Awards are invited from all current tenure-track junior faculty who are members of ACS and the ACS Division of Computers in Chemistry. Postdoctoral researchers in transition to faculty appointments may also be considered. Selection criteria will include the novelty and importance of the work to be presented, as well as the level of Departmental support as indicated by a letter of support by the Chair or Chair designee. To apply for an award for the ACS National Meeting In Philadelphia, PA, Aug. 17-21, 2008, an extended abstract of the work (no more than 2 pages) and the letter of departmental support should be sent to carlos.simmerling ~~ gmail.com IMPORTANT: EXTENDED ABSTRACT AND SUPPORT LETTER MUST BE RECEIVED BY 5PM EASTERN TIME ON MARCH 7, 2008. Applicants will receive email confirmation of receipt of materials. If you do not receive confirmation by March 10, 2008, please contact the organizer immediately by telephone (see below). In addition, you must submit your normal abstract to the "HP Outstanding Junior Faculty Award" symposium on the OASYS system (the COMP OASYS deadline is March 17, 2008 for the Philadelphia ACS Meeting) More information on awards offered by the ACS COMP division can be found on the web site at http://membership.acs.org/c/Comp/awards.html Carlos Simmerling Chair, ACS COMP Division Awards Committee Professor, Department of Chemistry Stony Brook University Stony Brook, NY 11794-3400 631-384-9248 From owner-chemistry@ccl.net Tue Mar 4 01:57:01 2008 From: "carlos simmerling carlos.simmerling%x%stonybrook.edu" To: CCL Subject: CCL: Final call for 2008 ACS COMP Emerging Technology Awards Message-Id: <-36400-080303190746-26708-rXdqdtMnKkLZzJg9IdbP4A[A]server.ccl.net> X-Original-From: "carlos simmerling" Date: Mon, 3 Mar 2008 19:07:43 -0500 Sent to CCL by: "carlos simmerling" [carlos.simmerling#%#stonybrook.edu] Please share this with anyone that has exciting work to share! We encourage people to enter any new technology related to computational chemistry. $1,000 prize to be awarded at the ACS national meeting, Philadelphia, PA. The Computers in Chemistry Division (COMP) of the ACS will hold the annual Symposium on Emerging Technologies in Computational Chemistry at the American Chemical Society National Meeting, Philadelphia, PA, Aug. 17-21 2008. The objective of the symposium is to stimulate, reward, and publicize methodological advances in computational chemistry. The talks will be evaluated at the meeting by a panel of experts on the quality of the presentation, and the impact that the research will have on the future of computational chemistry and allied sciences. The symposium is ideal for presenting your latest and best research on new techniques, applications and software development. Schrodinger, Inc., sponsors a $1,000 prize for the best talk at the symposium. All are invited to participate. To participate, it is necessary to submit a regular short ACS abstract via http://oasys.acs.org/ . It is also necessary to also email a longer (~1000-word) abstract to the organizer. The talks must be original and not be repeats of talks at other ACS symposia. The long abstracts will be evaluated, and those individuals selected for an oral presentation at the symposium will be notified. Applications for the Emerging Technologies Symposium that cannot be accepted will be rescheduled in one of the other COMP sessions at the meeting. Long abstracts must be sent by e-mail to carlos.simmerling-at-gmail.com Please use a subject of "ACS Emerging Tech Abstract". THE LONG ABSTRACT MUST BE SENT BY 5PM EASTERN TIME ON FRIDAY, MARCH 7, 2008. The short abstract must be submitted to OASYS by the normal deadline of March 17, 2008. You will receive a confirmation of receipt of your application via email. Please contact the organizer immediately if you do not receive confirmation by March 10. More information on awards offered by the ACS COMP division can be found on the web site at http://membership.acs.org/c/Comp/awards.html Carlos Simmerling Chair, ACS COMP Division Awards Committee Professor, Department of Chemistry Stony Brook University Stony Brook, NY 11794-3400 631-632-1336 From owner-chemistry@ccl.net Tue Mar 4 03:14:00 2008 From: "Guanna Li gnli^dicp.ac.cn" To: CCL Subject: CCL:G: =?gb2312?B?Q0NMo7pHo7puZWVkIGEgcHJvZ3JhbSBmb3IgdmlicmF0aW9uIGFuYWx5c2lz?= Message-Id: <-36401-080304025312-26533-lSavQdbgNqz9rAZl5pJVWQ .. server.ccl.net> X-Original-From: "Guanna Li" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="gb2312" Date: Tue, 4 Mar 2008 15:55:20 +0800 Mime-Version: 1.0 Sent to CCL by: "Guanna Li" [gnli ~~ dicp.ac.cn] Dear Alcides, Thank you for your advance. i have gaussianview, but it just can visualizing vibrations, what data i want to get is the vibration assignment exactly , gv only can see the molecular is moving. any advice is welcome! ------------------ Guanna Li 2008-03-04 Best wishes -------------- 2008-03-04 Best wishes Guanna Li State Key Laboratory of Catalysis Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road, Dalian 116023, China Tel: +86-411-8437 9302 Email: gnli|a|dicp.ac.cn From owner-chemistry@ccl.net Tue Mar 4 04:48:01 2008 From: "William F. Coleman wcoleman*_*wellesley.edu" To: CCL Subject: CCL:G: =?UTF-8?B?Q0NM77yaR++8mm5lZWQ=?= a program for vibration analysis Message-Id: <-36402-080304044427-5594-Dz/DSR6zbs1p1wuH+j+Abw__server.ccl.net> X-Original-From: "William F. Coleman" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Tue, 04 Mar 2008 04:08:53 -0500 MIME-Version: 1.0 Sent to CCL by: "William F. Coleman" [wcoleman-*-wellesley.edu] "CCL Subscribers" on Tuesday, March 04, 2008 at 2:55 AM -0500 wrote: > i have gaussianview, but it just can visualizing vibrations, what data i >want to get is the vibration assignment exactly , gv only can see the >molecular is moving I am not exactly sure what you mean by vibrational assignment - the frequency, the symmetry? If you open a log or chk file from Gaussian in GaussView, the first thing you should see is a table of vibrational frequencies, intensities, and any other vibrational information you have chosen to calculate. Additionally, if you display the IR spectrum in GaussView, clicking on any peak will give you the calculated frequency and intensity. Other information such as the symmetries and force constants are given in the log file. Cheers, Flick _______________ William F. Coleman Professor of Chemistry Wellesley College Wellesley MA 02481 on leave 2007-08 - please contact via email only wcoleman[#]wellesley.edu www.wellesley.edu/Chemistry/colemanw.html Editor, JCE WebWare and JCE Featured Molecules http://www.jce.divched.org/JCEDLib/WebWare/ http://jchemed.chem.wisc.edu/JCEWWW/Features/MonthlyMolecules/index.html From owner-chemistry@ccl.net Tue Mar 4 05:58:00 2008 From: "Philippe Carbonniere philippe.carbonniere .. univ-pau.fr" To: CCL Subject: CCL:G: need a program for vibration analysis Message-Id: <-36404-080304035439-23207-ZkaVtlIUU8mG8nThDa7NDQ(~)server.ccl.net> X-Original-From: Philippe Carbonniere Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Tue, 04 Mar 2008 09:03:33 +0100 MIME-Version: 1.0 Sent to CCL by: Philippe Carbonniere [philippe.carbonniere*|*univ-pau.fr] Hi ! What do you mean by "vibrational analysis3 ? If you wish to visualize gaussian vibrational data, you can use Molden =20 for instance. Hope this helps, Philippe Carbonniere Quoting "Guanna Li gnli#dicp.ac.cn" : > > Sent to CCL by: "Guanna Li" [gnli%%dicp.ac.cn] > Dear all, > I use Gaussian to do frequency calculation, and i want to =20 > find a program which can do vibration analysis, anybody who knows =20 > please help me! Thank you ! > > -------------- > 2008-03-03 > Best wishes > > Guanna Li > Email: gnli a dicp.ac.cn > > > > -=3D This is automatically added to each message by the mailing script =3D= -> > > From owner-chemistry@ccl.net Tue Mar 4 06:32:00 2008 From: "Sherin Falah shireen.alfalah*yahoo.com" To: CCL Subject: CCL: Structure of few compounds Message-Id: <-36405-080304062650-24332-OTHfpc18JIMSvql3MpGjaw#,#server.ccl.net> X-Original-From: "Sherin Falah" Date: Tue, 4 Mar 2008 06:26:46 -0500 Sent to CCL by: "Sherin Falah" [shireen.alfalah(~)yahoo.com] Dear CCL users, I am looking for the structure of some compounds but I can not find them. I would be very grateful if someone can provide me with the chemical structure for these compounds. The compounds are: 1. Aminochlorothenoxazin 2. dipanone 3. prolidine 4. hexalgon Thanks in advance. Best regards, Shireen Falah From owner-chemistry@ccl.net Tue Mar 4 07:07:01 2008 From: "Pablo Echenique echenique.p=-=gmail.com" To: CCL Subject: CCL: Coupled Cluster and MP4 in peptides Message-Id: <-36406-080304063401-28020-EJ4m2V8823Mu+aqG9j+44A/./server.ccl.net> X-Original-From: "Pablo Echenique" Content-Type: multipart/alternative; boundary="----=_Part_2818_31297947.1204624069862" Date: Tue, 4 Mar 2008 10:47:49 +0100 MIME-Version: 1.0 Sent to CCL by: "Pablo Echenique" [echenique.p-#-gmail.com] ------=_Part_2818_31297947.1204624069862 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear CCLers, In my group, at the University of Zaragoza, we are planning to build a new cluster to perform high-level QC calculations. Meaning CCSD, CCSD(T), MP4(SDQ) and MP4, with basis sets (Dunning's, for example) of, say, double-= , triple- and quadruple-zeta quality (if possible). To begin with, we are interested in capped peptide systems with 1 or 2 residues. Being Tryptophan the largest natural residue, the largest peptide we need to deal with is probably the 2-Tryptophan. A 1-Tryptophan has 17 1st-row atoms and 12 hydrogens, while a 2-Tryptophan has 31 1st-row atoms and 21 hydrogens (assuming formyl and amide cappings). We would like to calculate single-point energies, gradients and maybe secon= d derivatives of the energy of these systems using the aforementioned levels of the quantum chemical theory. We would thank any data regarding the hardware requirements to perform thes= e calculations, meaning minimum RAM memory, disk space and 1-node CPU/wall-clock time. As well as the relation of these requirements with the different existing codes. This will help us choose the best architecture for the new cluster. Thank you very much in advance. --=20 Pablo Echenique Instituto de Biocomputaci=F3n y F=EDsica de los Sistemas Complejos (BIFI) Departamento de F=EDsica Te=F3rica Universidad de Zaragoza Pedro Cerbuna 12, 50009 Zaragoza Spain Tel.: +34 976761260 Fax: +34 976761264 echenique.p/./gmail.com http://www.pabloechenique.com ------=_Part_2818_31297947.1204624069862 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Dear CCLers,

In my group, at the University of Zaragoza, we are plan= ning to build a new cluster to perform high-level QC calculations. Meaning = CCSD, CCSD(T), MP4(SDQ) and MP4, with basis sets (Dunning's, for exampl= e) of, say, double-, triple- and quadruple-zeta quality (if possible).

To begin with, we are interested in capped peptide systems with 1 or 2 = residues. Being Tryptophan the largest natural residue, the largest peptide= we need to deal with is probably the 2-Tryptophan. A 1-Tryptophan has 17 1= st-row atoms and 12 hydrogens, while a 2-Tryptophan has 31 1st-row atoms an= d 21 hydrogens (assuming formyl and amide cappings).

We would like to calculate single-point energies, gradients and maybe s= econd derivatives of the energy of these systems using the aforementioned l= evels of the quantum chemical theory.

We would thank any data regard= ing the hardware requirements to perform these calculations, meaning minimu= m RAM memory, disk space and 1-node CPU/wall-clock time. As well as the rel= ation of these requirements with the different existing codes.

This will help us choose the best architecture for the new cluster.
=
Thank you very much in advance.

--
Pablo Echen= ique

Instituto de Biocomputaci=F3n y
F=EDsica de los Sistemas Com= plejos (BIFI)

Departamento de F=EDsica Te=F3rica
Universidad de Zaragoza
Pedro Cerbuna 12, 50009 Zaragoza
Spain

Tel.:   +34 976761260=
Fax:    +34 976761264

echenique.p/./gmail.com
http://www.pabloechenique.com ------=_Part_2818_31297947.1204624069862-- From owner-chemistry@ccl.net Tue Mar 4 08:31:00 2008 From: "zborowsk..chemia.uj.edu.pl" To: CCL Subject: CCL:G: =?iso-8859-2?Q?CCL=A3=BAG=A3=BAneed_a_program_for_vibration_analysis?= Message-Id: <-36407-080304082727-28930-KIZgy792kc6ArT6qtAI3HQ]=[server.ccl.net> X-Original-From: zborowsk[A]chemia.uj.edu.pl Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-2 Date: Tue, 4 Mar 2008 14:27:10 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: zborowsk!A!chemia.uj.edu.pl Hi Angelina The Gar2PED is one of the packages for calculating Potential Energy Distribution of vibrational modes from Gaussian output. But this program work correctly rather only with the set of the molecular fragments predefined in it. So I do not know if it is suitable for you. It depends on the structure of "your" molecule(s). What do you study?? PS. I do not know if Gar2ped is available now on the net. But if you want I can send it to you. Best regards > > Sent to CCL by: "Guanna Li" [gnli ~~ dicp.ac.cn] > Dear Alcides, > Thank you for your advance. i have gaussianview, but it just can > visualizing vibrations, what data i want to get is the vibration > assignment exactly , gv only can see the molecular is moving. > any advice is welcome! > ------------------ > Guanna Li > 2008-03-04 > Best wishes > > -------------- > 2008-03-04 > Best wishes > > Guanna Li > > State Key Laboratory of Catalysis > Dalian Institute of Chemical Physics > Chinese Academy of Sciences > > 457 Zhongshan Road, Dalian 116023, China > > Tel: +86-411-8437 9302 > Email: gnli##dicp.ac.cn> > > -- Krzysztof Zborowski Faculty of Chemistry Jagiellonian University 3 Ingardena Street 30-060 Krakow Poland phone: +48(12)632-4888 ext. 2064 or 2067 fax: +48(12)634-05-15 email: zborowsk*chemia.uj.edu.pl gg 3817259 skype kzys70 From owner-chemistry@ccl.net Tue Mar 4 09:10:01 2008 From: "Klon, Anthony aklon(0)pcop.com" To: CCL Subject: CCL: Structure of few compounds Message-Id: <-36408-080304085524-9806-aGysaQOCyA0HDksXHJj4Xw|-|server.ccl.net> X-Original-From: "Klon, Anthony" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Tue, 4 Mar 2008 07:53:08 -0500 MIME-Version: 1.0 Sent to CCL by: "Klon, Anthony" [aklon---pcop.com] Hexalgon=20and=20aminochlorthenoxazin=20may=20be=20found=20in=20the=20PubC= hem=20database. Prolidine=20used=20to=20be=20there=20but=20was=20revoked.=20You=20can=20fi= nd=20it=20by=20searching eMolecules,=20which=20has=20a=20link=20to=20the=20revoked=20structure=20in= =20PubChem. http://pubchem.ncbi.nlm.nih.gov/ http://www.emolecules.com/ Tony Anthony=20E.=20Klon Research=20Scientist Molecular=20Modeling Pharmacopeia P.O.=20Box=205350 Princeton,=20NJ=2008543-5350 609.452.3676 -----Original=20Message----- > From:=20owner-chemistry+/-ccl.net=20[mailto:owner-chemistry+/-ccl.net]=20 Sent:=20Tuesday,=20March=2004,=202008=206:27=20AM To:=20Klon,=20Anthony Subject:=20CCL:=20Structure=20of=20few=20compounds Sent=20to=20CCL=20by:=20"Sherin=20=20Falah"=20[shireen.alfalah(~)yahoo.com= ] Dear=20CCL=20users,=20 I=20am=20looking=20for=20the=20structure=20of=20some=20compounds=20but=20I= =20can=20not=20find them.=20I=20would=20be=20very=20grateful=20if=20someone=20can=20provide=20= me=20with=20the chemical=20structure=20for=20these=20compounds.=20 The=20compounds=20are:=20 1.=20Aminochlorothenoxazin 2.=20dipanone 3.=20prolidine 4.=20hexalgon Thanks=20in=20advance.=20 Best=20regards,=20 Shireen=20Falah -=3D=20This=20is=20automatically=20added=20to=20each=20message=20by=20the=20= mailing=20script=20=3D- To=20recover=20the=20email=20address=20of=20the=20author=20of=20the=20mess= age,=20please=20change the=20strange=20characters=20on=20the=20top=20line=20to=20the=20+/-=20sign.=20= You=20can=20also look=20up=20the=20X-Original-From:=20line=20in=20the=20mail=20header. E-mail=20to=20subscribers:=20CHEMISTRY+/-ccl.net=20or=20use: =20=20=20=20=20=20http://www.ccl.net/cgi-bin/ccl/send_ccl_message E-mail=20to=20administrators:=20CHEMISTRY-REQUEST+/-ccl.net=20or=20use =20=20=20=20=20=20http://www.ccl.net/cgi-bin/ccl/send_ccl_message Subscribe/Unsubscribe:=20 =20=20=20=20=20=20http://www.ccl.net/chemistry/sub_unsub.shtml Before=20posting,=20check=20wait=20time=20at:=20http://www.ccl.net Job:=20http://www.ccl.net/jobs=20 Conferences:=20http://server.ccl.net/chemistry/announcements/conferences/ Search=20Messages:=20http://www.ccl.net/htdig=20=20(login:=20ccl,=20Passwo= rd: search) If=20your=20mail=20bounces=20from=20CCL=20with=205.7.1=20error,=20check: =20=20=20=20=20=20http://www.ccl.net/spammers.txt RTFI:=20http://www.ccl.net/chemistry/aboutccl/instructions/ ________________________________________________________________________ Scanned=20by=20IBM=20Email=20Security=20Management=20Services=20powered=20= by MessageLabs. ________________________________________________________________________ ________________________________________________________________________ Scanned=20by=20IBM=20Email=20Security=20Management=20Services=20powered=20= by=20MessageLabs. ________________________________________________________________________ From owner-chemistry@ccl.net Tue Mar 4 11:20:00 2008 From: "Troy Wymore wymore!=!psc.edu" To: CCL Subject: CCL: ACS COMP Division: Combining Computational Chemistry w/ Bioinformatics Message-Id: <-36409-080304110646-676-9286R8MfinECTAe7UrbDWQ .. server.ccl.net> X-Original-From: "Troy Wymore" Date: Tue, 4 Mar 2008 11:06:43 -0500 Sent to CCL by: "Troy Wymore" [wymore]_[psc.edu] The Computers in Chemistry Division (COMP) of the ACS will hold a symposium on "Combining Computational Chemistry with Sequence-Based Bioinformatics for Structure-Function-Activity Relationships" at the American Chemical Society National Meeting, Philadelphia, PA, Aug. 17-21 2008. Organizers: Troy Wymore National Resource for Biomedical Supercomputing Charles L. Brooks III University of Michigan This symposium will be a mix of invited and submitted presentations focused on research discoveries that combine results from computational chemistry methods with those from sequence-based bioinformatics to construct structure-function and/or structure-activity relationships. Ideally, the presentations will focus on results that could not be obtained by either discipline alone or at the very least is less robust without the combination of both disciplines. An example would be analyzing the properties of conserved and family-specific amino acid residues (obtained through multiple sequence alignment and phylogenetic analysis) through molecular dynamics simulations, docking, and other physical chemistry-based calculations. The calculations may be examining critical processes important for biomolecular function and activity such as conformational transitions, protein folding, ligand binding and enzyme activity that can be correlated with evolutionarily conserved features of the biomolecular system. Results that highlight the importance of residues beyond the first sphere of the active site are of particular interest. In some cases, the biomolecular function might not require residues to be conserved and we encourage submissions of this nature as well. Abstracts can be submitted through http://oasys.acs.org The deadline for submission is March 17, 2008 Any questions about the symposium can be directed to Troy Wymore (wymore..psc.edu). From owner-chemistry@ccl.net Tue Mar 4 12:39:00 2008 From: "Jens Thomas j.m.h.thomas|-|dl.ac.uk" To: CCL Subject: CCL: CCP1 Meeting - Molecular Modelling: Tools, GUIs and Visualisation Message-Id: <-36410-080304122921-20601-uKxuO21mT4w7naKs8bEBYw_-_server.ccl.net> X-Original-From: Jens Thomas Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 04 Mar 2008 17:25:38 +0000 MIME-Version: 1.0 Sent to CCL by: Jens Thomas [j.m.h.thomas.- -.dl.ac.uk] Molecular Modelling: Tools, GUIs and Visualisation - 11th - 13th March 2008 This is just to announce that the program is now available on the meeting webpage: http://www.ccp1.ac.uk/chemtoolsmeet/ The program includes links to the various projects that will be presenting at the meeting. Best wishes, Jens Thomas Original announcement: This is to announce a CCP1 meeting looking at graphical interfaces, visualisation and tools for molecular modelling in general, but with the focus towards electronic structure. There are a large number of graphical interfaces and associated tools for working with electronic structure and molecular mechanics/dynamics codes in use in the computational chemistry community today. Many of these tools do similar jobs, but all have their own specialities, strengths and weaknesses. The aim of this meeting is to bring together the developers and users of these tools to: - raise awareness of the existing software tools and capabilities. - allow users to give the developers feedback on what is needed and which areas are not being sufficiently covered. - explore novel ways of visualising molecular data and other tasks. - provide an opportunity to discuss collaborations. We already have speakers confirmed from projects including OpenBabel, Avogadro, Molekel, Jmol, Molpro, Aten, Zeobuilder, cclib, GaussSum, The CCP1GUI, GAMESS, and GAMESS-UK. The meeting will be held at the Holiday Inn in Runcorn, Cheshire, from 11th-13th March (starting after lunch on the 11th and running through to lunch on the 13th). The afternoon of the 13th will be reserved for developers to run tutorials/practicals at Daresbury Laboratory. From owner-chemistry@ccl.net Tue Mar 4 13:14:00 2008 From: "Gokcen Eren rasemus###gmail.com" To: CCL Subject: CCL: Structure of few compounds Message-Id: <-36411-080304111520-2988-KfWDD30Xx/DNBQNADrfKhA(~)server.ccl.net> X-Original-From: "Gokcen Eren" Content-Type: multipart/mixed; boundary="----=_Part_21004_21234005.1204643549858" Date: Tue, 4 Mar 2008 17:12:29 +0200 MIME-Version: 1.0 Sent to CCL by: "Gokcen Eren" [rasemus:+:gmail.com] ------=_Part_21004_21234005.1204643549858 Content-Type: multipart/alternative; boundary="----=_Part_21005_30705557.1204643549858" ------=_Part_21005_30705557.1204643549858 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline You can find hexalgon in attached file. You can search the others with SciFinder i found it there. On Tue, Mar 4, 2008 at 1:26 PM, Sherin Falah shireen.alfalah*yahoo.com < owner-chemistry,,ccl.net> wrote: > > Sent to CCL by: "Sherin Falah" [shireen.alfalah(~)yahoo.com] > Dear CCL users, > I am looking for the structure of some compounds but I can not find them. > I would be very grateful if someone can provide me with the chemical > structure for these compounds. > The compounds are: > 1. Aminochlorothenoxazin > 2. dipanone > 3. prolidine > 4. hexalgon > > Thanks in advance. > > Best regards, > Shireen Falah> > > ------=_Part_21005_30705557.1204643549858 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline

 

You can find hexalgon in attached file. You can search the others with SciFinder i found it there.

On Tue, Mar 4, 2008 at 1:26 PM, Sherin Falah shireen.alfalah*yahoo.com <owner-chemistry,,ccl.net> wrote:

Sent to CCL by: "Sherin  Falah" [shireen.alfalah(~)yahoo.com]
Dear CCL users,
I am looking for the structure of some compounds but I can not find them. I would be very grateful if someone can provide me with the chemical structure for these compounds.
The compounds are:
1. Aminochlorothenoxazin
2. dipanone
3. prolidine
4. hexalgon

Thanks in advance.

Best regards,
Shireen Falah



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//////////////////////////////////////////////////////////////////////////// //////////////8BAP7/AwoAAP////8GCQIAAAAAAMAAAAAAAABGFwAAAE1pY3Jvc29mdCBXb3Jk IEJlbGdlc2kACgAAAE1TV29yZERvYwAQAAAAV29yZC5Eb2N1bWVudC44APQ5snEAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAA== ------=_Part_21004_21234005.1204643549858-- From owner-chemistry@ccl.net Tue Mar 4 14:17:01 2008 From: "Zaki Safi zaki.safi(_)gmail.com" To: CCL Subject: CCL: Protona affinities and basicities Message-Id: <-36412-080304115008-2129-yCZ2b+aj/uX9jjbBzCO1WA[*]server.ccl.net> X-Original-From: "Zaki Safi" Content-Type: multipart/alternative; boundary="----=_Part_13901_3391798.1204643031595" Date: Tue, 4 Mar 2008 17:03:51 +0200 MIME-Version: 1.0 Sent to CCL by: "Zaki Safi" [zaki.safi_-_gmail.com] ------=_Part_13901_3391798.1204643031595 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear CCL users, I am looking for the experimental values of the proton affinities and basicities of the 5-methyl imidazolidine-2,4-dione (dithione). I would be very grateful if someone can provide me with these values. -- ===== ===== ===== ===== Dr. Zaki Safi Assist. Prof. of Quantum Chemistry, Chemistry Department, Faculty of Science Al-Azhar University-Gaza P. O. Box 1277 Gaza, Palestine Tel: 00972-8-2824010/20, Ext:1163, Fax:2823180. ------=_Part_13901_3391798.1204643031595 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Dear CCL users,
I am looking for the experimental values of the proton affinities and basicities of the 5-methyl imidazolidine-2,4-dione (dithione). I would be very grateful if someone can provide me with these values.
 


--
=====      =====
        =====      =====
Dr. Zaki Safi
Assist. Prof. of Quantum Chemistry,
Chemistry Department, Faculty of Science
Al-Azhar University-Gaza
P. O. Box 1277 Gaza, Palestine
Tel: 00972-8-2824010/20, Ext:1163, Fax:2823180.
------=_Part_13901_3391798.1204643031595-- From owner-chemistry@ccl.net Tue Mar 4 14:52:00 2008 From: "Soren Eustis soren###jhu.edu" To: CCL Subject: CCL:G: Simple Batch/Queue Software for Linux 64-bit/ Gaussian 03 Message-Id: <-36413-080304144108-25233-CG8zR3PVOngQlLBthqM11w]^[server.ccl.net> X-Original-From: "Soren Eustis" Date: Tue, 4 Mar 2008 14:41:04 -0500 Sent to CCL by: "Soren Eustis" [soren- -jhu.edu] I have relied on WebMo to handle my queuing for G03 on windows. Now that I have G03 running on my Linux EM64T, I would love to get that working as well. However, for the time being it has eluded me. In the mean time, can anyone recommend a simple batch program that will work under Linux (OpenSuse to be specific). The Gaussian manual talks about NQS... Thanks in advance. Soren Eustis Department of Chemistry Johns Hopkins University From owner-chemistry@ccl.net Tue Mar 4 16:32:01 2008 From: "Antony Williams tony(!)chemspider.com" To: CCL Subject: CCL: Structure of few compounds Message-Id: <-36414-080304145544-983-FZTTgN0XTxTZiNiJgQRmpg*server.ccl.net> X-Original-From: "Antony Williams" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Tue, 4 Mar 2008 14:01:20 -0500 MIME-Version: 1.0 Sent to CCL by: "Antony Williams" [tony()chemspider.com] You can check ChemSpider by name searches Hexalgon can be found on ChemSpider here: http://www.chemspider.com/21015 I cannot find prolidine. I can find Prolidon: http://www.chemspider.com/Chemical-Structure.5773.html Triprolidine: http://www.chemspider.com/Chemical-Structure.4445597.html Aminochlorothenoxazin can be found here http://www.chemspider.com/17877 . Note the name has NOT been validated. Best wishes. Antony Williams, URL: www.chemspider.com Email: antony.williams::chemspider.com Phone: (919) 341-8375 Mobile: (919) 201-1516 Fax: (919) 300-5321 =20 CONFIDENTIALITY NOTICE Unless expressly stated otherwise, this message is confidential and is intended for the addressee(s) only. If you are not an addressee, please inform the sender immediately or contact feedback::chemspider.com. =20 > -----Original Message----- > From: owner-chemistry::ccl.net [mailto:owner-chemistry::ccl.net] > Sent: Tuesday, March 04, 2008 6:27 AM > To: Antony Williams > Subject: CCL: Structure of few compounds >=20 >=20 > Sent to CCL by: "Sherin Falah" [shireen.alfalah(~)yahoo.com] > Dear CCL users, > I am looking for the structure of some compounds but I can not find them. > I would be very grateful if someone can provide me with the chemical > structure for these compounds. > The compounds are: > 1. Aminochlorothenoxazin > 2. dipanone > 3. prolidine > 4. hexalgon >=20 > Thanks in advance. >=20 > Best regards, > Shireen Falah >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script =3D->=20>=20>=20>=20>=20>=20>=20>=20>=20 From owner-chemistry@ccl.net Tue Mar 4 19:40:01 2008 From: "Guanna Li gnli,dicp.ac.cn" To: CCL Subject: CCL:G: need a program for vibration analysis Message-Id: <-36415-080304193740-11911-io7H1cU0cAxPbFq0LQOL3w::server.ccl.net> X-Original-From: "Guanna Li" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="gb2312" Date: Wed, 5 Mar 2008 08:39:41 +0800 Mime-Version: 1.0 Sent to CCL by: "Guanna Li" [gnli{:}dicp.ac.cn] Dear all, Thanks very much for all advice! I think I didn't make it clear. what i want is, e.g. open the log file in gaussianview, we can see the frequency, intensity, but i want a program can give information about which vibrational mode(bend,torsion, etc.) it including? -------------- 2008-03-05 Best wishes Guanna Li Email: gnli()dicp.ac.cn From owner-chemistry@ccl.net Tue Mar 4 21:06:00 2008 From: "Guanna Li gnli_+_dicp.ac.cn" To: CCL Subject: CCL: need a program for vibration analysis Message-Id: <-36416-080304210319-19046-z187qAQwDF80cOIMjlR6Sw++server.ccl.net> X-Original-From: "Guanna Li" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="gb2312" Date: Wed, 5 Mar 2008 10:05:27 +0800 Mime-Version: 1.0 Sent to CCL by: "Guanna Li" [gnli:+:dicp.ac.cn] Dear Professor Wang, Thank you very much for your help! I am a graduate student in group 503, and my supervisor is professor Can Li. Best wishes 2008-03-05 Guanna Li Email: gnli _ dicp.ac.cn From owner-chemistry@ccl.net Tue Mar 4 21:56:01 2008 From: "Guanna Li gnli..dicp.ac.cn" To: CCL Subject: CCL:G: need a program for vibration analysis Message-Id: <-36417-080304215330-17550-qux4cyQyhyfP3wfFx46IzA|server.ccl.net> X-Original-From: "Guanna Li" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="gb2312" Date: Wed, 5 Mar 2008 10:55:37 +0800 Mime-Version: 1.0 Sent to CCL by: "Guanna Li" [gnli|-|dicp.ac.cn] Dear all, I really appreciate everybody's help! I did a test, and freq=internalmodes option in gaussian is usefull. -------------- 2008-03-05 Best wishes Guanna Li Email: gnli[-]dicp.ac.cn