From owner-chemistry@ccl.net Tue Feb 5 04:20:00 2013 From: "=?ISO-8859-1?Q?R=F3bert_Kiss?= rkiss:-:mcule.com" To: CCL Subject: CCL: 1-Click Scaffold Hop Message-Id: <-48170-130205041650-23325-Wz6suKBK28uktpjVWiPO+w]|[server.ccl.net> X-Original-From: =?ISO-8859-1?Q?R=F3bert_Kiss?= Content-Type: multipart/alternative; boundary=e89a8f3bae0f11528f04d4f6abed Date: Tue, 5 Feb 2013 10:16:43 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?R=F3bert_Kiss?= [rkiss(-)mcule.com] --e89a8f3bae0f11528f04d4f6abed Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Identify completely new active scaffolds and leads with a single click! Introducing: 1-Click Scaffold Hop After the great success of 1-Click Docking, mcule.com, the online drug discovery platform, is pleased to announce the release of 1-Click Scaffold Hop, the easiest online solution for ligand-based drug discovery. Draw a known active ligand and jump to a new active scaffold by clicking on Scaffold Hop! To understand why the two molecules are similar click on =93Visualize similarity=94 when browsing the results. Try 1-Click Scaffold Hopnow! It is FREE. Have a nice hopping! Robert Kiss CSO, mcule.com rkiss(-)mcule.com --- About mcule.com: DO EARLY PHASE DRUG DISCOVERY LIGHTNING FAST! Mcule.com is the online drug discovery platform. It offers a unique solution for pharma and biotech companies by providing molecular modelling tools and the highest quality purchasable compound database. --e89a8f3bae0f11528f04d4f6abed Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Identify completely new active scaffolds and leads with a single click!
=
Introducing: 1-Click Scaffold Hop

After the great success of 1-Click Docking, mcule.com, the online drug discovery platform, is p= leased to announce the release of 1-Click Scaffold Hop, the ea= siest online solution for ligand-based drug discovery.

Draw a known active ligand and jump to a new active scaffold by clickin= g on Scaffold Hop! To understand why the two molecules are similar click on= =93Visualize similarity=94 when browsing the results.

Try 1-Click Scaffold Hop now! It is FREE.

Have a nice hopping!

Robert Kiss
CSO, mcule.com
rkiss(-)mcule.com

---

About mcule.com:

DO EARLY PHASE DRUG DISCOVERY LIGHTNING FAST!

Mcule.com is the online drug discovery platform. It offers a un= ique solution for pharma and biotech companies by providing molecular model= ling tools and the highest quality purchasable compound database. --e89a8f3bae0f11528f04d4f6abed-- From owner-chemistry@ccl.net Tue Feb 5 12:14:00 2013 From: "BEHTASH, SINA behtash!A!email.sc.edu" To: CCL Subject: CCL: COSMO vs COSMO-RS Message-Id: <-48171-130205120916-30449-qq4Rs4kjzMf+Uy8MtHgamg,,server.ccl.net> X-Original-From: "BEHTASH, SINA" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 5 Feb 2013 17:08:57 +0000 MIME-Version: 1.0 Sent to CCL by: "BEHTASH, SINA" [behtash ~ email.sc.edu] Dear Andreas, Thank you for your detailed response. I confirm that GReaction-COSMO-RS-Water - GReaction-gas in my calculations is exactly the dG_solvation difference of reactants and products at BP-TZVP-COSMO-RS level. To make the calculations more optimal, this time, I also optimized the reactants and products structures in COSMO using b3-lyp/QZVP and dielectric constant of water at 298 K (78.39). Next, to make inputs for COSMO-RS calculations, I used the COSMO/b3lyp optimized structures to run COSMO single-point energy calculations at BP-TZVP level and dielectric constant of infinity. Also, for dG_reaction calculation, I performed frequency calculations and used Freeh to calculate the partition functions but as you explained, the correction term cancels out in "GReaction-COSMO-RS-Water - GReaction-gas" . Finally, the result shows that, GReaction-COSMO - GReaction-gas= -14.6 Kcal/mol and GReaction-COSMO-RS-Water - GReaction-gas= -0.2 Kcal/mol Considering that COSMO-RS takes the hydrogen-bonding, non-electrostatic and electrostatic interactions into account, I agree that my COSMO-RS results should be more reliable than COSMO results; however, I would like to make sure that my method of calculations (which is first, optimization in gas phase using b3lyp, then optimization in COSMO using b3lyp and finally using the COSMO/b3lyp optimized structure to run COSMO/BP-TZVP single-point energy calculations) is a correct approach. I was wondering if you have any other suggestions to make these calculations more optimal? Thank you! Best regards Sina -------------------------------------- Sina Behtash Ph.D. Student Department of Chemical Engineering University of South Carolina Phone: (803)777-0611 Email: behtash:+:email.sc.edu ________________________________________ > From: owner-chemistry+behtash==email.sc.edu:+:ccl.net [owner-chemistry+behtash==email.sc.edu:+:ccl.net] on behalf of Andreas Klamt klamt/acosmologic.de [owner-chemistry:+:ccl.net] Sent: Thursday, January 31, 2013 6:35 AM To: BEHTASH, SINA Subject: CCL: COSMO vs COSMO-RS Sent to CCL by: Andreas Klamt [klamt=cosmologic.de] Dear Sina, there are several potential reasons for the large difference. On the one hand you used qute different basis sets for the COSMO calculations at eps=78 and the eps=infinity calculations. Admittedly I do not expect that this changes the results too much. I am not completely sure how you did the COSMO-RS reaction calculation. Did you use the thermodynamic cycle inserting the gasphase reaction energy from the b3-lyp and a def2-QZVP calculation? If so, then the latter result, i.e. GReaction-COSMO-RS-Water - GReaction-gas= -2.05 Kcal/mol should be nothing else than the dG_solvation difference of educts and products on BP-TZVP-COSMO-RS level, since GReaction-gas cancels out. Can you just check and confirm that? Please note that bare COSMO (unlike other implicit solvation models) is not parameterized for giving optimal dG-solvation values. It just trets the electrostatic component, and not the dispersion, and other non-electrosttic contributions. Hence you cannot expect good quantitative results for dG_hydrtion from using bare COSMO. COSMO-RS is my recommended method to take all these things into account. Finally it should be noted that the recommended procedure for dG_reaction calculation requires to include the vibr., rot. and transl. free energy contributions in the gasphase, which will be very important for a reaction in which the number of particles changes from 1 to 4. These can be calculated for exmple with the freeH tool in TURBOMOLE. But this contribution would appear in the gasphase as well as in the liquid phase and thus should not influence your differential results. In summary, I do not find your result too surprising. The more relible answer should be the COSMO-RS answer, but please note that your calculations are still suboptimal. Best regards Andreas Am 31.01.2013 00:13, schrieb Sina Behtash behtash!=!email.sc.edu: > Sent to CCL by: "Sina Behtash" [behtash ~ email.sc.edu] > > I am using both COSMO (implemented in Turbomole 6.0) and COSMOtherm/COSMO-RS to calculate the solvent effects on the free energy of reaction for the following reaction: > > Glucose --> HMF + 3 H2O > > First, I optimized all the reactants and products in the gas phase using b3-lyp and a def2-QZVP basis set. Next, assuming that the geometry does not change significantly in the presence of water, I used the optimized structure to run a COSMO single-point energy calculation with the same basis set and dielectric constant of water at 298 K which is 78.39. According to the COSMO calculation, > > GReaction-COSMO - GReaction-gas= -15.2 Kcal/mol > > Next, in order to generate relevant input for COSMO-RS calculations, I ran another COSMO single-point energy calculation using the BP functional and TZVP basis set. Then I used COSMOtherm/Reactions and the BP-TZVP data base to run COSMO-RS calculations for my reaction at T=298K. > > The result shows that, > > GReaction-COSMO-RS-Water - GReaction-gas= -2.05 Kcal/mol > > I was expecting that for water, the COSMO and COSMO-RS calculations should give almost the same result. However, in this case the difference in the effect of water on the free energy of reaction is around 13 Kcal/mol. Can anyone explain to me why the difference is so large? Im wondering if the effects of hydrogen bonding and electrostatic interactions can be this significant. > > Sina Behtash > Ph.D. Student > Department of Chemical Engineering > University of South Carolina > Phone: (803)777-0611 > Email: behtash-$-email.sc.edu> > > -- Prof. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH & Co. KG Imbacher Weg 46 D-51379 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt*cosmologic.de web www.cosmologic.de [University address: Inst. of Physical and Theoretical Chemistry, University of Regensburg] HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamthttp://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 Tue Feb 5 14:23:00 2013 From: "Andrew Dalke dalke#%#dalkescientific.com" To: CCL Subject: CCL: ANN: chemfp-1.1 Message-Id: <-48172-130205141234-3505-PQGpG1Rv7ihgw84RWXtJxA-*-server.ccl.net> X-Original-From: Andrew Dalke Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Tue, 5 Feb 2013 20:12:28 +0100 Mime-Version: 1.0 (Apple Message framework v1257) Sent to CCL by: Andrew Dalke [dalke:+:dalkescientific.com] I've just released chemfp-1.1, a package for cheminformatics fingerprints. This is the last time that the most recent commercial version and the no-cost versions are identical. In the future, new features will go to paying customers first, and after a year or two will be released to the general public at no cost. Both versions are distributed under the MIT/BSD license. For more information see the product page at http://chemfp.com/ . What does chemfp contain? ------------------------- There are command-line programs to: - create fingerprints using the OpenEye, Open Babel, or RDKit toolkits - extract fingerprints from tags of an SD file - do high-performance Tanimoto similarity searches, including k-nearest neighbors These are based on the 'chemfp' Python library, also included, which has a documented, public API that you can use for your own code. The fingerprints are stored in the FPS fingerprint exchange format documented at http://code.google.com/p/chem-fingerprints/wiki/FPS . With it you can, for example, write your own program to generate fingerprints and use chemfp for the Tanimoto search. What's new in chemfp-1.1? ------------------------- The biggest improvement is performance. In a benchmark of the NxN symmetric search, the new code is about 30 times faster than chemfp-1.0 on the same hardware, because it now knows how to use the POPCNT instruction, to use OpenMP across multiple cores (4 in this case), and to take advantage of symmetry. This combined with the existing sub-linear search algorithm means you can find the upper-triangle sparse similarity matrix of 100,000 PubChem fingerprints (881 bits) with a threshold of 0.8 in about 15 seconds on a modern desktop computer. For the full list of changes, including API additions and bug fixes, see the CHANGELOG at http://code.google.com/p/chem-fingerprints/source/browse/CHANGELOG Andrew Dalke dalke:_:dalkescientific.com From owner-chemistry@ccl.net Tue Feb 5 15:04:00 2013 From: "Mohammad Rezaei rezaei.4 ~~ osu.edu" To: CCL Subject: CCL: Questions about Force Fields in TINKER Message-Id: <-48173-130205130658-23159-S5jOet1eALF4GYQDvYxv2w-$-server.ccl.net> X-Original-From: "Mohammad Rezaei" Date: Tue, 5 Feb 2013 13:06:57 -0500 Sent to CCL by: "Mohammad Rezaei" [rezaei.4*osu.edu] Dear all, I'm trying to calculate the typical coefficients (like: VdW, Hydrogen bonding, etc) for a dataset including complexes of proteins and small molecules using polarizable FF. Since the force fields in TINKER were mentioned to be different in TINKER manual (e.g. AMOEBA for small molecules, and AMOEBABIO for proteins), is it possible to use the same FF for the complex? or is it better to use the two FFs (AMOEBA and AMOEBABIO) for their corresponding ligand / protein simultaneously? (I'm not sure if it is possible, and how). I appreciate very much your valuable comments in this regard. M. Rezaei From owner-chemistry@ccl.net Tue Feb 5 15:39:00 2013 From: "Guenter Grethe ggrethe||att.net" To: CCL Subject: CCL: CINF-RSC Scholarships for Scientific Excellence Message-Id: <-48174-130205144747-14349-m2yU3/7eGv3l7OzlN6mBDg .. server.ccl.net> X-Original-From: "Guenter Grethe" Date: Tue, 5 Feb 2013 14:47:46 -0500 Sent to CCL by: "Guenter Grethe" [ggrethe() att.net] 2013 CINF Scholarship for Scientific Excellence Sponsored by the Royal Society of Chemistry The scholarship program of the Division of Chemical Information (CINF) of the American Chemical Society (ACS) funded by the Royal Society of Chemistry (RSC) is designed to reward graduate and postdoctoral students in chemical information and related sciences for scientific excellence and to foster their involvement in CINF. Up to three scholarships valued at $1,000 each will be presented at the 246th ACS National Meeting in Indianapolis, IN, September 8 September 12, 2013. Applicants must be enrolled at a certified college or university, and they will present a poster during the Welcoming Reception of the Division on Sunday evening at the National Meeting. Additionally, they will have the option to also show their poster at the Sci-Mix session on Monday night. Abstracts for the poster must be submitted electronically through PACS, the abstract submission system of ACS. To apply, please inform the Chair of the selection committee, Guenter Grethe at ggrethe^_^att.net that you are applying for a scholarship. Submit your abstract to http://abstracts.acs.org using your ACS ID. If you do not have an ACS ID, follow the registration instructions and submit your abstract in the CINF program for the session CINF Scholarship for Scientific Excellence. PACS will be open for abstract submissions from January 21 to March 18, 2013. Additionally, please send a 2,000-word abstract describing the work to be presented in electronic form to the Chair of the selection committee by June 30, 2013. Any questions related to applying for one of the scholarships should be directed to the same e-mail address. Winners will be chosen based on contents, presentation and relevance of the poster and they will be announced during the reception. The contents shall reflect upon the students work and describe research in the field of cheminformatics and related sciences. Winning posters will be marked Winner of RSC-CINF Scholarship for Scientific Excellence at the poster session. Guenter Grethe From owner-chemistry@ccl.net Tue Feb 5 16:13:00 2013 From: "Stefan Grimme grimmes---uni-muenster.de" To: CCL Subject: CCL: COSMO vs. COSMO-RS Message-Id: <-48175-130205160603-7401-NJCERXyXLJgcOr6eoKMvog#,#server.ccl.net> X-Original-From: "Stefan Grimme" Date: Tue, 5 Feb 2013 16:06:02 -0500 Sent to CCL by: "Stefan Grimme" [grimmes^^uni-muenster.de] Dear Sina, you can improve your thermodynamic calculations by consistently accounting for London dispersion effects. They are included in COSMO-RS but NOT in B3LYP so your gas phase thermodynamic data are inconsistent with you solvent corrections. There are various dispersion corrections for B3LYP around and I would suggest to use our D3. I have discussed this topic specifically using COSMO-RS in two recent papers: "Supramolecular Binding Thermodynamics by Dispersion-Corrected Density Functional Theory", Chem. Eur. J., (2012), 18, 9955-9964 and "Comment on: On the Accuracy of DFT Methods in Reproducing Ligand Substitution Energies for Transition Metal Complexes in Solution: The Role of Dispersive Interactions" by H. Jacobsen and L. Cavallo", ChemPhysChem, (2012), 13, 1407-1409 Cheers! Stefan ____________________________________________________________ Prof. Dr. Stefan Grimme (grimme]*[thch.uni-bonn.de) Chair of Theoretical Chemistry Mulliken Center for Theoretical Chemistry University of Bonn Beringstr. 4, D-53115 Bonn, Germany http://www.thch.uni-bonn.de/tc/ ____________________________________________________________ From owner-chemistry@ccl.net Tue Feb 5 17:04:00 2013 From: "Devang Sachdev dsachdev:nvidia.com" To: CCL Subject: CCL: Try MD/QC apps on Tesla K20 GPUs Message-Id: <-48176-130205170317-22081-4TrzJLB8RWfRgH6qPKwOpQ_+_server.ccl.net> X-Original-From: "Devang Sachdev" Date: Tue, 5 Feb 2013 17:03:16 -0500 Sent to CCL by: "Devang Sachdev" [dsachdev_._nvidia.com] Hi I wanted to share updates with you about the NVIDIA's GPU Test Drive program for computational chemistry: You can now try MD/QC applications remotely on latest Tesla K20 GPU Accelerators for free - www.nvidia.com/GPUTestDrive Read the benchmark reports on how the Tesla K20 GPUs can increase application performance over the previous generation Fermi GPUs, and CPUs alone. AMBER 12 Benchmark Report - http://bit.ly/AMBER_GPU NAMD 2.9 Benchmark Report - http://bit.ly/NAMD_GPU LAMMPS Benchmark Report - http://bit.ly/LAMMPS_GPU GROMACS 4.6 Benchmark Reprot - http://bit.ly/GROMACS_GPU To sign up for the free and easy Tesla K20 GPU test drive today and try AMBER on Tesla K20, all you need to do is: 1. Register on www.nvidia.com/GPUTestDrive 2. Log in to a remote cluster with Tesla K20 GPUs (we will send you instructions). 3. Run your application to get speed-up results for Tesla K20. Several MD/QC applications are already pre-loaded on the cluster. You can also try your code. Thanks Devang Sachdev Sr. Product Manager GPU Computing - NVIDIA http://www.linkedin.com/in/devangsachdev