From owner-chemistry@ccl.net Tue Apr 24 01:15:01 2007 From: "nihcho/./barc.gov.in" To: CCL Subject: CCL: Is cartesian coordinates available? Message-Id: <-34110-070423020658-7931-1uz/jOJurGVF/2q5chEdgQ+*+server.ccl.net> X-Original-From: nihcho*barc.gov.in Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 23 Apr 2007 10:35:46 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: nihcho]^[barc.gov.in Dear friends, I would like to have cartesian coordinates (xyz) of the following series of molecules. Can anybody help me? Molecules are 1) cucurbit[6]uril 2) cucurbit[7]uril 3) cucurbit[8]uril 4) cuclodextrin (alpha,beta and gama) 5) calix[n]arene thanks Niharendu Choudhury Scientific Officer Theoretical Chemistry Section BARC, Mumbai 400 085 ------------------------------------------------- From owner-chemistry@ccl.net Tue Apr 24 05:44:01 2007 From: "=?ISO-8859-1?Q?J=E9r=F4me?= Kieffer jerome.kieffer!=!terre-adelie.org" To: CCL Subject: CCL:G: ECP for IR spectrum Message-Id: <-34111-070424052504-3925-ZC30RqnCW/yWeEezLTlCMg * server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?J=E9r=F4me?= Kieffer" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 24 Apr 2007 11:24:43 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?J=E9r=F4me?= Kieffer" [jerome.kieffer!=!terre-adelie.org] Dear CCLers, I am usually calculating the IR spectrum of organic molecules using gaussian03 with B3LYP/6-31G(d). Now I have to studdy a molecule containing many iodine atoms, increasing very much the calculation time. What kind of ECP would you recommand to do this type of job ? of course I would like to use ECP only on iodine, and keep C,H,O,N atoms fully described. Thank you for your help. Regards. Jerome Kieffer -- Jerome Kieffer From owner-chemistry@ccl.net Tue Apr 24 06:49:01 2007 From: "Soren Eustis soren.:.jhu.edu" To: CCL Subject: CCL: Photodetachment Cross-Section Message-Id: <-34112-070424044900-32702-8bfiS8nOZVYQF0AvdkhSyA() server.ccl.net> X-Original-From: "Soren Eustis" Content-language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_003E_01C7862B.80095740" Date: Tue, 24 Apr 2007 04:46:18 -0400 MIME-Version: 1.0 Sent to CCL by: "Soren Eustis" [soren!A!jhu.edu] This is a multipart message in MIME format. ------=_NextPart_000_003E_01C7862B.80095740 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit There was a post recently about the calculation of a two-photon absorption process. How does one obtain information about the photodetachment (single-photon) cross-section for a molecule? Soren N. Eustis Graduate Research Assistant Department of Chemistry Johns Hopkins University 3400 N. Charles Street Baltimore, MD 21218 (410) 516-4675 (office) (410) 925-5167 (cell) (410) 516-8420 (fax) soren]*[jhu.edu ------=_NextPart_000_003E_01C7862B.80095740 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

There was a post recently about the calculation of = a two-photon absorption process. How does one obtain information = about the photodetachment (single-photon) cross-section for a molecule?

Soren N. Eustis

Graduate Research Assistant

Department of Chemistry

Johns Hopkins University

3400 N. Charles Street

Baltimore, MD 21218

(410) 516-4675 (office)

(410) 925-5167 (cell)

(410) 516-8420 (fax)

soren]*[jhu.edu

------=_NextPart_000_003E_01C7862B.80095740-- From owner-chemistry@ccl.net Tue Apr 24 07:49:00 2007 From: "Jens Spanget-Larsen spanget%a%ruc.dk" To: CCL Subject: CCL:G: ECP for IR spectrum Message-Id: <-34113-070424074723-28682-srbtU9tcrPhrCfIzvNuN/w]![server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 24 Apr 2007 13:47:15 +0200 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget a ruc.dk] Dear Jerome, I have performed G03 B3LYP-calculations on iodine-compounds by using the CEP121 basis set (for all atoms) with some success. But I prefer DGDZVP. - What kind of compounds are you considering? Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget##ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ Jérôme Kieffer jerome.kieffer!=!terre-adelie.org wrote: > Sent to CCL by: "=?ISO-8859-1?Q?J=E9r=F4me?= Kieffer" [jerome.kieffer!=!terre-adelie.org] > > Dear CCLers, > > I am usually calculating the IR spectrum of organic molecules using > gaussian03 with B3LYP/6-31G(d). Now I have to studdy a molecule > containing many iodine atoms, increasing very much the calculation time. > What kind of ECP would you recommand to do this type of job ? of course I > would like to use ECP only on iodine, and keep C,H,O,N atoms fully > described. > > Thank you for your help. Regards. > > Jerome Kieffer From owner-chemistry@ccl.net Tue Apr 24 08:32:01 2007 From: "Taye Beyene Demisse sene3095]=[yahoo.com" To: CCL Subject: CCL:G: Frequency calculations Message-Id: <-34114-070424082433-13304-72eM4X6LDugVaKI+PJ4vIg::server.ccl.net> X-Original-From: "Taye Beyene Demisse" Date: Tue, 24 Apr 2007 08:24:30 -0400 Sent to CCL by: "Taye Beyene Demisse" [sene3095]=[yahoo.com] Dear CCL subscribers, peace for all you. I am calculating frequency of compounds which can polymerize. I used one publishe paper as a standard, but the results for the dimmers is completely different from the results on the paper. Those of you who calculated frequencies for polymers please help me if there is any method of calculation using G03(RHF and ROHF for reuced and oxidized forms) along with the minimal basis set STO-3G. If it is possible please send me related papers that used G03 to calculate frequencies(Thermodynamic properties). Thank you very much. Taye. From owner-chemistry@ccl.net Tue Apr 24 09:11:00 2007 From: "Alba Chimirri chimirri ~~ pharma.unime.it" To: CCL Subject: CCL: 10th European Catalyst User Group Meeting Message-Id: <-34115-070424052749-4193-IY0NyV7+o80CQH+/S8gyow]~[server.ccl.net> X-Original-From: "Alba Chimirri" Date: Tue, 24 Apr 2007 05:27:42 -0400 Sent to CCL by: "Alba Chimirri" [chimirri#%#pharma.unime.it] Please join us at the 10th European Catalyst User Group Meeting to be held at the Universit degli Studi di Messina, Sicily, Italy. This meeting will be held on Thursday October 4th, 2007. The registration and agenda for this event has been posted at the URL below. http://www.accelrys.com/products/catalyst/usergroup/2007/EU/index.html We would also like to invite you to present your work at this meeting; you can indicate on the electronic registration form if you would like to give a presentation. We will be updating the agenda as more speakers are added to the list. The past success of these meetings has been based on the diverse scientific contributions from the Catalyst user community and invited speakers. Please register for this event so that we can determine the numbers of attendees and speakers, and continue the successful tradition of the Catalyst UGM. This user group marks the first meeting where Accelrys will be presenting Catalyst in its new environment as a part of the Discovery Studio platform. Accelrys scientists will review the pharmacophore modelling solutions in the current Discovery Studio 1.7 and will also unveil the new functionalities in the upcoming 2.0 release, allowing you to combine pharmacophores with library design and analysis, and QSAR tools. The Catalyst User Group Meeting is a great opportunity to get to know other users, speak with the Accelrys Development and Marketing team, and share your results with colleagues, both from academia as well as industry. Join us at this stimulating forum to add your input into future enhancements to our pharmacophore modelling solutions I hope to see you there, Alba Chimirri University of Messina From owner-chemistry@ccl.net Tue Apr 24 10:04:00 2007 From: "Gustavo Seabra gustavo.seabra##gmail.com" To: CCL Subject: CCL: Photodetachment Cross-Section Message-Id: <-34116-070424095330-3333-s0jrMEsDJcN5WUWzoWsWzQ^^server.ccl.net> X-Original-From: Gustavo Seabra Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 24 Apr 2007 09:53:07 -0400 MIME-Version: 1.0 Sent to CCL by: Gustavo Seabra [gustavo.seabra^^^gmail.com] Soren Eustis soren.:.jhu.edu wrote: > > There was a post recently about the calculation of a two-photon > absorption process. How does one obtain information about the > photodetachment (single-photon) cross-section for a molecule? > Hi Soren, You can do that using electron propagator theory. Basically, the cross section of photoionization is proportional to the fourier transform of the Dyson orbital for that specific ionization. For more details, take a look at: J. Chem. Phys., 121, 4143 (2004) J. Chem. Phys., 123, 114105 (2005) All the best, Gustavo. From owner-chemistry@ccl.net Tue Apr 24 10:40:00 2007 From: "Luis Simon luissimonrubio]^[hotmail.com" To: CCL Subject: CCL: Stokes law and stochastic dynamics Message-Id: <-34117-070424102132-17580-vHYAmQBS5HBcIx1DWBfqWA ~~ server.ccl.net> X-Original-From: "Luis Simon" Date: Tue, 24 Apr 2007 10:21:27 -0400 Sent to CCL by: "Luis Simon" [luissimonrubio|,|hotmail.com] I have find out that for stochastic dynamics it is possible to calculate the atomic frictional coefficient of a solvent from stokes law knowing its viscosity and vdw radius, assuming that solvent molecules are spherical. But could someone please tell me if some modifications to stokes law should be done in the case of non-spherical molecules? Any reference about the subject? Thanks in Advanced: Luis From owner-chemistry@ccl.net Tue Apr 24 11:14:00 2007 From: "=?ISO-8859-1?Q?J=E9r=F4me?= Kieffer jerome.kieffer###terre-adelie.org" To: CCL Subject: CCL:G: ECP for IR spectrum Message-Id: <-34118-070424093410-24392-BiL21x1fDol12XcdN5tYxQ#%#server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?J=E9r=F4me?= Kieffer" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 24 Apr 2007 15:33:44 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?J=E9r=F4me?= Kieffer" [jerome.kieffer##terre-adelie.org] Dear Jens, Thank you very much for your help. >I have performed G03 B3LYP-calculations on iodine-compounds by using the >CEP121 basis set (for all atoms) with some success. But I prefer DGDZVP. I just discovered DGDZVP is the same basis set as used in DGauss (I dont use DGauss for this as it does not include hybrid DFT: Only GGA & LDA). >- What kind of compounds are you considering? I am considering the IR vibration of a keton conjugated with a phenyl group and the effect of the substitution of iodin on this phenyl group. Except iodine, all atoms are from the second row, a typycal organic product. Regards. -- Jerome Kieffer From owner-chemistry@ccl.net Tue Apr 24 11:49:01 2007 From: "Taye Beyene Demisse sene3095[#]yahoo.com" To: CCL Subject: CCL: Help Message-Id: <-34119-070424111143-18135-iXdCCVzPCADFWmys5e0WPQ]*[server.ccl.net> X-Original-From: "Taye Beyene Demisse" Date: Tue, 24 Apr 2007 11:11:39 -0400 Sent to CCL by: "Taye Beyene Demisse" [sene3095 ~~ yahoo.com] Hello dear CCLs? I am calculating frequency of some compounds which can polymerize. When I am calculating properties for the redox process results other than the monomers is different from a result of other scholars(used as standard for my calc). If you know, how many electrons are removed from the dimmers to calculate the frequency of the oxidized species? (I removed only one electron from the monomer). Please help me if you know it. Thanks. Taye. From owner-chemistry@ccl.net Tue Apr 24 12:36:00 2007 From: "Alex Allardyce aa###chemaxon.com" To: CCL Subject: CCL: ChemAxon's User Group Meeting - 13-14 June, Budapest, Hungary - Program announcement Message-Id: <-34120-070424123351-11061-T6e7N3FE/I0xmQSJ/bwuvg~!~server.ccl.net> X-Original-From: Alex Allardyce Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 24 Apr 2007 17:33:59 +0100 MIME-Version: 1.0 Sent to CCL by: Alex Allardyce [aa+/-chemaxon.com] Please excuse cross postings. The program is now available for ChemAxon's 2007 User Group Meeting which will be held on Wednesday and Thursday, June 13-14 at the Gellert Hotel Spa in Budapest, Hungary. The meeting will preceded by a training day on June 12. The meeting will feature presentations from ChemAxon users, a lightning presentation session and exhibition from ChemAxon Partners and the latest updates on product developments as well as discussion sessions for shaping future product development. Preceding the meeting will be a training day (June 12th) for beginner to advanced level users to become familiar with ChemAxon's end user applications. As usual we will have extensive social events for attendees to mix and enjoy. To find out more about the meeting and training day, register or submit a poster abstract (open until June 1st) and view the program, please visit: http://www.chemaxon.com/UGM/07/index.html See you there. Alex Confirmed speakers: Barry Bunin, Collaborative Drug Discovery Christophe Cleva, Merck Serono Elodie Dubus, Aureus Pharma Dragos Horvath, CNRS Paul Laffort, CNRS Andrew Lemon, Edge Consultancy Takahiro Ohshima, Teijin Pharma Stephan Schurer, TSRI Patrick Walters, Vertex Pharmaceuticals Seong Jae Yu, FMC Corp ChemAxon Partners (tbc) - see partner listing here: http://www.chemaxon.com/partners/integrators.html -- Alex Allardyce Dir. Marketing, ChemAxon Cell-US: 1-857-544-0541 skype: alex_allardyce From owner-chemistry@ccl.net Tue Apr 24 13:15:01 2007 From: "Tae-Yun Park taeyun0000(-)gmail.com" To: CCL Subject: CCL:G: Gaussian with GPU-based computation ?? Message-Id: <-34121-070424054643-6823-x3mP5+jP8Fd5l0jGtHKbAA ~~ server.ccl.net> X-Original-From: "Tae-Yun Park" Date: Tue, 24 Apr 2007 05:46:38 -0400 Sent to CCL by: "Tae-Yun Park" [taeyun0000[]gmail.com] Dear all, Sorry if this question has already been posted, as I'm currently unable to search the CCL archives. I wonder if anyone tried to perform GPU computing for the computational chemistry applications, e.g., Gaussian. It seems that the GPU-based computing is farely effective for the complicated scientific & engineering computation. The Gaussian package has already been parallelized through Linda for muli-CPU environment, but I wonder if any trial has been made under GPU-computation environment. Any information related to this subject would be appreciated. I'll summerize the answers. Thanks in advance, Tae-Yun From owner-chemistry@ccl.net Tue Apr 24 14:31:01 2007 From: "John Stone johns*ks.uiuc.edu" To: CCL Subject: CCL:G: Gaussian with GPU-based computation ?? Message-Id: <-34122-070424142951-7798-d+ZdTwaTG3lMTXB8NZdTZg**server.ccl.net> X-Original-From: John Stone Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Tue, 24 Apr 2007 13:29:15 -0500 Mime-Version: 1.0 Sent to CCL by: John Stone [johns*o*ks.uiuc.edu] Hi, We're presently doing work on GPU acceleration with NVIDIA's CUDA system. One of the minor barriers to using GPUs for codes like Gaussian (until the next hardware generation anyway) is the current lack of double precision arithmetic. We are hearing that GPUs with double precision arithmetic will become available later this year. There are a number of techniques for performing higher precision floating point arithmetic based on single precision hardware. For calculations where only a small fraction of the arithmetic requires double precision, a software emulation approach would work very well. Given that the GPU hardware is evolving extremely rapidly, it is probably simplest for codes that require extensive use of double precision arithmetic to plan on using the upcoming double precision hardware and not worry about emulating it in software. The existing CUDA toolkit can be used to develop code for hardware with double precision arithmetic, though it will be executed in single precision on current generation GPUs. I have posted materials from a guest lecture I gave last month for those that are curious about this topic: http://www.ks.uiuc.edu/Research/vmd/projects/ece498/lecture/ Cheers, John Stone johns**ks.uiuc.edu On Tue, Apr 24, 2007 at 05:46:38AM -0400, Tae-Yun Park taeyun0000(-)gmail.com wrote: > > Sent to CCL by: "Tae-Yun Park" [taeyun0000[]gmail.com] > > Dear all, > > Sorry if this question has already been posted, as I'm currently unable to search the CCL archives. > > I wonder if anyone tried to perform GPU computing for the computational chemistry applications, e.g., Gaussian. It seems that the GPU-based computing is farely effective for the complicated scientific & engineering computation. > > The Gaussian package has already been parallelized through Linda for muli-CPU environment, but I wonder if any trial has been made under GPU-computation environment. > > Any information related to this subject would be appreciated. > > I'll summerize the answers. > > Thanks in advance, > > Tae-Yun> > -- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns**ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 From owner-chemistry@ccl.net Tue Apr 24 15:06:00 2007 From: "Jerome Kieffer jerome.Kieffer a terre-adelie.org" To: CCL Subject: CCL: Gaussian with GPU-based computation ?? Message-Id: <-34123-070424150421-23072-ZHHJcmgC3+9rAcbpENCHvg#server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15 Date: Tue, 24 Apr 2007 21:04:01 +0200 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [jerome.Kieffer:terre-adelie.org] On Tue, 24 Apr 2007 05:46:38 -0400 "Tae-Yun Park taeyun0000(-)gmail.com" wrote: > It seems that the GPU-based computing is farely effective for the complicated scientific & engineering computation. The problem with GPU is their low precision : you cannot get a SCF convergence to down 1E-8 with a processor (GPU) which is only able to calculate (event very quickly) at 1E-6, the precision needed for 3D. More precisely this is related to the size of the object manipulated in 3D rendering and in quantum chemistry and the size of the mantissa of floatting point numbers. The precision of GPU has increased recently but is it usable for research now ? Regards. -- Jérôme KIEFFER From owner-chemistry@ccl.net Tue Apr 24 15:41:01 2007 From: "Konrad Hinsen hinsen-.-cnrs-orleans.fr" To: CCL Subject: CCL: Stokes law and stochastic dynamics Message-Id: <-34124-070424151239-28521-c0g2G/XovTLb254l54O5Sw*server.ccl.net> X-Original-From: "Konrad Hinsen" Date: Tue, 24 Apr 2007 15:12:35 -0400 Sent to CCL by: "Konrad Hinsen" [hinsen(!)cnrs-orleans.fr] On 24.04.2007, at 16:21, Luis Simon luissimonrubio]^[hotmail.com wrote: > I have find out that for stochastic dynamics it is possible to calculate the atomic frictional coefficient > of a solvent from stokes law knowing its viscosity and vdw radius, assuming that solvent molecules > are spherical. But could someone please tell me if some modifications to stokes law should be done > in the case of non-spherical molecules? Any reference about the subject? Stokes' law applies to spherical objects with a well-defined surface that are immersed in a liquid, under certain conditions on its size and velocity (low Reynolds number flow). It may accidentally be valid for atoms surrounded by a solvent, just like atomic polarizations happen to be rather well described by macroscopic polarization laws, though no one knows why. But even if that is true, it is far > from obvious that generalizations of Stokes' law can also be transferred to the atomic scale. BTW, the assumption of sphericity in Stokes' law applies to the particle for which the friction is calculated, not to the solvent, which is described by a continuum anyway. Konrad. From owner-chemistry@ccl.net Tue Apr 24 16:19:01 2007 From: "Jeff Hammond jeff.science*_*gmail.com" To: CCL Subject: CCL:G: Gaussian with GPU-based computation ?? Message-Id: <-34125-070424155633-28581-l3qT1mT3l0zAqT4B8+J9Pw%%server.ccl.net> X-Original-From: Jeff Hammond Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 24 Apr 2007 13:58:50 -0500 MIME-Version: 1.0 Sent to CCL by: Jeff Hammond [jeff.science]^[gmail.com] First, the general subject is covered here: http://www.gpgpu.org/. There isn't an easy way to let Gaussian use a GPU except to link with a GPU BLAS library. Last time I checked, however, those BLAS libraries only do single precision because that is what the GPU works with. Electronic structure calculations are pretty meaningless with single precision. When GPU's are required to do double precision calculations, the performance is rather modest. You can google "GPU blas" if you want to see what has been done so far. Finally, very few people run Gaussian on their desktop where they have a powerful GPU. Most calculations run on clusters which don't have video cards, so the utility of a GPU port for any scientific code is fairly limited. A more likely scenario is use of accelerator cards with scientific computing in mind (http://www.clearspeed.com). Jeff Tae-Yun Park taeyun0000(-)gmail.com wrote: > Sent to CCL by: "Tae-Yun Park" [taeyun0000[]gmail.com] > > Dear all, > > Sorry if this question has already been posted, as I'm currently unable to search the CCL archives. > > I wonder if anyone tried to perform GPU computing for the computational chemistry applications, e.g., Gaussian. It seems that the GPU-based computing is farely effective for the complicated scientific & engineering computation. > > The Gaussian package has already been parallelized through Linda for muli-CPU environment, but I wonder if any trial has been made under GPU-computation environment. > > Any information related to this subject would be appreciated. > > I'll summerize the answers. > > Thanks in advance, > > Tae-Yun> > > > From owner-chemistry@ccl.net Tue Apr 24 21:02:00 2007 From: "Axel Kohlmeyer qmmmworkshop,+,cmm.chem.upenn.edu" To: CCL Subject: CCL: 2nd CMM QM/MM Workshop at the University of Pennsylvania Message-Id: <-34126-070424194230-23441-5dsmcS9Ycgl/xCm0IsNF1w|a|server.ccl.net> X-Original-From: "Axel Kohlmeyer" Date: Tue, 24 Apr 2007 19:42:26 -0400 Sent to CCL by: "Axel Kohlmeyer" [qmmmworkshop]*[cmm.chem.upenn.edu] Dear Colleague. We cordially invite you to register for attending the: 2nd CMM 'Users Meet Developers' Workshop on QM/MM Simulations August 24th to 26th in Philadelphia, PA * Goals The primary goals of this workshop are to encourage communication between different QM/MM approaches and implementations, exchange ideas about solutions to common problems and to discuss ways to make QM/MM calculations more accessible for newcomers to the field. To this effect, we would like to bring together active QM/MM code developers and experienced users. * Format The workshop will consist of selected presentations on current methods and applications of QM/MM simulations. The schedule will give a lot of room for discussions. We will start on Friday, August 24th in the 'early' morning (8.30am) and close on Sunday, August 26th around noon. Please note, that those are the 3 days directly after the 2007 Summer ACS meeting in Boston (which closes on Thursday). * Pre-Registration and Participation The workshop will be sponsored by the LRSM through which we can provide accommodation in the form of a block of pre-reserved (double occupation) hotel rooms in a hotel that is a nice 20min walk (or a 5min bus ride) from the Penn campus and the lecture hall. The maximum number of participants and presenters, however, is limited due to limited funding, the size of the lecture hall, and to maintain the informal atmosphere which leaves much room for fruitful discussions. Interested parties can contact stating their interest to participate, their background, affiliation and existing experience and - if applicable - suggesting a tentative title for a presentation. In order to bring in as many people as possible, we also kindly ask you to indicate whether you would be able to find (and/or fund) accommodation on your own. If notified in advance we can negotiate a discounted rate at the conference hotel. * Venue and Program The workshop will be held in the "Carolyn Hoff Lynch Lecture Hall" in the Cret wing of the Penn chemistry complex. The web page for the workshop is at http://www.cmm.upenn.edu/qmmm2007.html and currently still contains the details for last year's workshop (for your information). The web page will be updated as new information for this year's event becomes available. * Deadline Please respond to qmmmworkshop^^^cmm.chem.upenn.edu until: May 12th 2007 Confirmation of your attendance will be sent out shortly after that date. We are hoping to meet you soon in Philadelphia. On behalf of the CMM and the organizers, Axel Kohlmeyer. -- ======================================================================= Dr. Axel Kohlmeyer akohlmey^^^cmm.chem.upenn.edu http://www.cmm.upenn.edu Associate Director - Center for Molecular Modeling - U. of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= From owner-chemistry@ccl.net Tue Apr 24 22:15:02 2007 From: "Reaz Uddin riaasuddin__yahoo.com" To: CCL Subject: CCL: how to interpret Fred docking scores Message-Id: <-34127-070424154442-18207-Z5aO9c0AjjmDEDWTgx5RBw-.-server.ccl.net> X-Original-From: Reaz Uddin Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-244747004-1177440257=:49219" Date: Tue, 24 Apr 2007 11:44:17 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Reaz Uddin [riaasuddin,,yahoo.com] --0-244747004-1177440257=:49219 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi, Fred scores are the energy terms, so you can interpret them as, the more the negative value, the rank'd be the best. Thanks REAZ "sriram boppana sri.boppana%%gmail.com" wrote: Sent to CCL by: "sriram boppana" [sri.boppana#gmail.com] Hi All Does any one knows to how to interpret docking results of FRED(openeye)what is best score and what is least score. the out put file shows in -ve valuse. It would be very helpful if someone could Explain. Thanks Srihttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtREAZUDDIN Research Scholar Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, (M/C 781) University of Illinois at Chicago 833 S. Wood St. Chicago, IL 60612 Email: ruddin[-]uic.edu, riaasuddin[-]yahoo.com Web: http://medchem.pharm.uic.edu/ --------------------------------- Ahhh...imagining that irresistible "new car" smell? Check outnew cars at Yahoo! Autos. --0-244747004-1177440257=:49219 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit

Hi,

Fred scores are the energy terms, so you can interpret them as, the more the negative value, the rank'd be the best.

Thanks

REAZ

"sriram boppana sri.boppana%%gmail.com" <owner-chemistry[-]ccl.net> wrote:

Sent to CCL by: "sriram boppana" [sri.boppana#gmail.com]
Hi All

Does any one knows to how to interpret docking results of FRED(openeye)what is best score and what is least score. the out put file shows in -ve valuse.

It would be very helpful if someone could Explain.

Thanks
Sri

http://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/cgi-bin/ccl/send_ccl_message
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http://www.ccl.net/spammers.txt

REAZUDDIN
Research Scholar
Department of Medicinal Chemistry and Pharmacognosy,
College of Pharmacy, (M/C 781)
University of Illinois at Chicago
833 S. Wood St.
Chicago, IL 60612
Email: ruddin[-]uic.edu, riaasuddin[-]yahoo.com
Web: http://medchem.pharm.uic.edu/

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