From owner-chemistry@ccl.net Wed Sep 29 03:16:00 2010 From: "Andreas Klamt klamt/a\cosmologic.de" To: CCL Subject: CCL:G: BSSE, COSMO and DFT Message-Id: <-42853-100929030854-30538-Bred89wwmnev8sg/AZCy/A|,|server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 29 Sep 2010 09:08:31 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt#cosmologic.de] Dear Juan, honestly spoken, I have no experience regarding the cross-effects of COSMO and counterpoise methods, but I do not expect severe conceptional problems, at least if outlying charge corrections are applied (which is not the case in Gaussian-COSMO), because the additional basis functions outside the cavity appearing in the counterpoise calculations may increase the outlying charge and hence may increase artifacts, if the outlying charge is not adequately corrected. Anyway, I do not recommend to do reactions or complex formations directly in solution, but to do the calculations in the gasphase (as good as you can afford, incl. vibr. corrections and counterpoise) and then use a solvation model (on a validated level of theory for the employed solvation model) in order to calculate the solvation free energies of educts and products. Combining the gasphase energy difference with the solvation energy difference gives the most reliable estimate of the reaction free energy in solution. (Needless to say, that I consider COSMO-RS as the best level to do the solvation free energies.) Best regards Andreas Am 28.09.2010 21:02, schrieb Juan C. Drosos jdrosos|*|gmail.com: > Sent to CCL by: "Juan C. Drosos" [jdrosos,+,gmail.com] > Dear Sirs. > > We would like to know if it is correct to apply , during a G03 energy > calculation (for a macromolecule-ligand system), the keywords BSSE > (counterpoise) and COSMO (scrf=COSMO) at the same time?. > We are concerned and confused because the trend in energies, when the > system was considered<>, was excellent and in agreement > with observed chemical phenomena. > But once the solvation was included, the results significantly > diverged and a total loss of chemical sense was observed. > > we used the functionals X3LYP and M06-2X with 6-311G(d,p) basis set. > > We would appreciate any comments. > > Best Regards. > > > -- PD. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH& Co. KG Burscheider Strasse 515 D-51381 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt:_:cosmologic.de web www.cosmologic.de HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt From owner-chemistry@ccl.net Wed Sep 29 04:43:00 2010 From: "Massimiliano Porrini mozz76%%gmail.com" To: CCL Subject: CCL: helical content time series Message-Id: <-42854-100928112047-9343-7eLbUZAueechymmo1cTGpA a server.ccl.net> X-Original-From: Massimiliano Porrini Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 28 Sep 2010 16:20:37 +0100 MIME-Version: 1.0 Sent to CCL by: Massimiliano Porrini [mozz76|-|gmail.com] Dear CCLers, Does anyone know anything about an application (or code) able to calculate the time series of the helical content of a peptide/protein by using the trajectory obtained from a MD run? Specifically I have got Amber10 trajectories, but in case they could be converted in PDB trajectories (or XYZ etc.) Any hint would be really appreciated. Many thanks in advance, Massimiliano -- Dr. Massimiliano Porrini Dr. P. E. Barran Research Group University of Edinburgh School of Chemistry Joseph Black Building West Mains Road Edinburgh, EH9 3JJ Tel: +44 (0) 131 650 7748 Fax: +44 (0) 131 650 6453 E-mail : mozz76%gmail.com or maxp%iesl.forth.gr From owner-chemistry@ccl.net Wed Sep 29 08:24:00 2010 From: "=?ISO-8859-1?Q?Xevi_Biarn=E9s_=28SISSA=29?= xbiarnes*sissa.it" To: CCL Subject: CCL: helical content time series Message-Id: <-42855-100929061804-22452-ExrwO94reD1H7Xp5+p4BGg]^[server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Xevi_Biarn=E9s_=28SISSA=29?= Content-Type: multipart/alternative; boundary=0016364ef2ce0e6b7a04916345ef Date: Wed, 29 Sep 2010 12:17:33 +0200 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Xevi_Biarn=E9s_=28SISSA=29?= [xbiarnes^-^sissa.it] --0016364ef2ce0e6b7a04916345ef Content-Type: text/plain; charset=ISO-8859-1 dear Massimiliano, you could try gromacs tools. in particular, do_dssp reads a trajectory file and computes the secondary structure for each time frame calling the dssp program. you will have to previously convert your trajectory to any of these formats: xtc trr trj gro g96 pdb cpt I suggest you to convert it to the binary compressed xtc format (for example with VMD). hope it helps. Xevi. On Tue, Sep 28, 2010 at 5:20 PM, Massimiliano Porrini mozz76%%gmail.com < owner-chemistry _ ccl.net> wrote: > > Sent to CCL by: Massimiliano Porrini [mozz76|-|gmail.com] > > Dear CCLers, > > Does anyone know anything about an application (or code) able to calculate > the > time series of the helical content of a peptide/protein by using > the trajectory obtained from a MD run? > > Specifically I have got Amber10 trajectories, but in case they could > be converted in PDB trajectories (or XYZ etc.) > > Any hint would be really appreciated. > > Many thanks in advance, > Massimiliano > > > -- > Dr. Massimiliano Porrini > Dr. P. E. Barran Research Group > University of Edinburgh > School of Chemistry > Joseph Black Building > West Mains Road > Edinburgh, EH9 3JJ > > Tel: +44 (0) 131 650 7748 > Fax: +44 (0) 131 650 6453 > > E-mail : mozz76/a\gmail.com or maxp/a\iesl.forth.gr> > > --0016364ef2ce0e6b7a04916345ef Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable dear Massimiliano,

you could try gromacs tools. in parti= cular, do_dssp=A0reads a trajectory file and computes the secondary structu= re for each=A0time frame calling the dssp program.

you will have to previously convert your trajectory to any of these formats= : xtc trr trj gro g96 pdb cpt

I suggest you to con= vert it to the binary compressed xtc format (for example with VMD).

hope it helps.


= Xevi.



On Tue, S= ep 28, 2010 at 5:20 PM, Massimiliano Porrini mozz76%%gmail.com <owner-chemistry _ ccl.net> wrote:

Sent to CCL by: Massimiliano Porrini [mozz76|-|gmail.com]

Dear CCLers,

Does anyone know anything about an application (or code) able to calculate = the
time series of the helical content of a peptide/protein by using
the trajectory obtained from a MD run?

Specifically I have got Amber10 trajectories, but in case they could
be converted in PDB trajectories (or XYZ etc.)

Any hint would be really appreciated.

Many thanks in advance,
Massimiliano


--
Dr. Massimiliano Porrini
Dr. P. E. Barran Research Group
University of Edinburgh
School of Chemistry
Joseph Black Building
West Mains Road
Edinburgh, EH9 3JJ

Tel: +44 (0) 131 650 7748
Fax: +44 (0) 131 650 6453

E-mail : mozz76/a\gmail.com<= /a> or maxp/a\iesl.forth= .gr



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--0016364ef2ce0e6b7a04916345ef-- From owner-chemistry@ccl.net Wed Sep 29 09:00:01 2010 From: "Thomas Exner thomas.exner- -uni-konstanz.de" To: CCL Subject: CCL: Protein-Ligand-Docking Software PLANTS Message-Id: <-42856-100929073643-30560-Tt7RyEhquIZHex2DXXYSFw|a|server.ccl.net> X-Original-From: Thomas Exner Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 29 Sep 2010 13:36:35 +0200 MIME-Version: 1.0 Sent to CCL by: Thomas Exner [thomas.exner:uni-konstanz.de] Dear CCLers, we would like to announce the release of a new version of our protein-ligand docking software PLANTS (Protein-Ligand ANT System). New features include additional constraints like SIFT and fixed scaffolds as well as a NMR docking mode, in which experimental data from trNOE and STD NMR spectroscopy can be used. Another highlight is the ligand-based approach pharmACOphore for the flexible alignment of multiple ligands. Last but not least, the structure preparation module SPORES was also updated with an improved structure recognition capacity and new features for the generation of protomers. A free version for non-profit organizations can be downloaded at http://www.tcd.uni-konstanz.de/. For commercial use, please contact the authors. Please, feel free to test it and sent us your comments. Thomas Exner University of Konstanz From owner-chemistry@ccl.net Wed Sep 29 09:34:00 2010 From: "Juan C. Drosos jdrosos . gmail.com" To: CCL Subject: CCL:G: BSSE, COSMO and DFT Message-Id: <-42857-100929090007-20366-0iJJwONwauzqU8L0Cs57tw:+:server.ccl.net> X-Original-From: "Juan C. Drosos" Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 29 Sep 2010 07:59:56 -0500 MIME-Version: 1.0 Sent to CCL by: "Juan C. Drosos" [jdrosos^gmail.com] We would like to add to the post some additional information regarding our initial post (included at the end of this post) We have tried other option wich is an optimization step using COSMO and then with that optmzd geometry a SCF calculation considering the BSSE via counterpoise to estimate each part energies. the results are in agreement (in trend) and better quantitatively (moderately) than just considering all calculations <>. in both cases X3LYP and M06-2X . Thanks in advance for all your cooperation Juan C Drosos. INITIAL POST. We would like to know if it is correct to apply , during a G03 energy calculation (for a macromolecule-ligand system), the keywords BSSE (counterpoise) and COSMO (scrf=COSMO) at the same time?. We are concerned and confused because the trend in energies, when the system was considered<>, was excellent and in agreement with observed chemical phenomena. But once the solvation was included, the results significantly diverged and a total loss of chemical sense was observed. we used the functionals X3LYP and M06-2X with 6-311G(d,p) basis set. We would appreciate any comments. Best Regards. From owner-chemistry@ccl.net Wed Sep 29 10:09:00 2010 From: "Cesar Millan pachequin###gmail.com" To: CCL Subject: CCL: helical content time series Message-Id: <-42858-100929092357-11410-G90lny6ybQ2kk5R0sZPlsw/a\server.ccl.net> X-Original-From: Cesar Millan Content-Type: multipart/alternative; boundary=00163649a099c51d21049165dea0 Date: Wed, 29 Sep 2010 08:23:11 -0500 MIME-Version: 1.0 Sent to CCL by: Cesar Millan [pachequin*_*gmail.com] --00163649a099c51d21049165dea0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Massimiliano. You could use simulaid (http://inka.mssm.edu/~mezei/simulaid/). Some features are: - Prepare a Ramachandran plot - Prepare dial plots for selected torsion angles - Perform the proline kink analysis of Visiers et al. as implemented in the program ProKink - Perform a variety of helix analyses (TRAJELIX) - Calculate pseudorotational angles - Calculate/plot DSSP Helix/Sheet assignments - Prepare circular variance map - Calculate correlation and covariance matrices over a trajectory Best regards Cesar On Wed, Sep 29, 2010 at 5:17 AM, Xevi Biarn=E9s (SISSA) xbiarnes*sissa.it < owner-chemistry=-=ccl.net> wrote: > dear Massimiliano, > > you could try gromacs tools. in particular, do_dssp reads a trajectory fi= le > and computes the secondary structure for each time frame calling the dssp > program. > > you will have to previously convert your trajectory to any of these > formats: xtc trr trj gro g96 pdb cpt > > I suggest you to convert it to the binary compressed xtc format (for > example with VMD). > > hope it helps. > > > Xevi. > > > > On Tue, Sep 28, 2010 at 5:20 PM, Massimiliano Porrini mozz76%%gmail.com < > owner-chemistry*ccl.net> wrote: > >> >> Sent to CCL by: Massimiliano Porrini [mozz76|-|gmail.com] >> >> Dear CCLers, >> >> Does anyone know anything about an application (or code) able to calcula= te >> the >> time series of the helical content of a peptide/protein by using >> the trajectory obtained from a MD run? >> >> Specifically I have got Amber10 trajectories, but in case they could >> be converted in PDB trajectories (or XYZ etc.) >> >> Any hint would be really appreciated. >> >> Many thanks in advance, >> Massimiliano >> >> >> -- >> Dr. Massimiliano Porrini >> Dr. P. E. Barran Research Group >> University of Edinburgh >> School of Chemistry >> Joseph Black Building >> West Mains Road >> Edinburgh, EH9 3JJ >> >> Tel: +44 (0) 131 650 7748 >> Fax: +44 (0) 131 650 6453 >> >> E-mail : mozz76/a\gmail.com or maxp/a\iesl.forth.gr >> >> >> >> -=3D This is automatically added to each message by the mailing script = =3D- >> E-mail to subscribers: CHEMISTRY*ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST*ccl.net or use>> >> >> > --=20 ############################ C=E9sar Mill=E1n Pacheco Instituto de Ciencias Fisicas Universidad Nacional Autonoma de Mexico email: cmp=-=uaem.mx pachequin=-=gmail.com --00163649a099c51d21049165dea0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear=A0Massimiliano.

You could use simulaid (http://inka.mssm.edu/~mezei/simulaid/). Some features are:

<= span class=3D"Apple-style-span" style=3D"border-collapse: collapse;">
--00163649a099c51d21049165dea0-- From owner-chemistry@ccl.net Wed Sep 29 16:13:00 2010 From: "Van Dam, Hubertus J HubertusJJ.vanDam(!)pnl.gov" To: CCL Subject: CCL:G: NWChem version 6.0 (Open Source) released Message-Id: <-42859-100929153818-8975-wfqkPnprcf1AmWVsjtCkkA^^^server.ccl.net> X-Original-From: "Van Dam, Hubertus J" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_FDD09CBD8676AE40957DCDAD24E9627A01889AE16766EMAIL04pnlg_" Date: Wed, 29 Sep 2010 12:38:09 -0700 MIME-Version: 1.0 Sent to CCL by: "Van Dam, Hubertus J" [HubertusJJ.vanDam . pnl.gov] --_000_FDD09CBD8676AE40957DCDAD24E9627A01889AE16766EMAIL04pnlg_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable We are pleased to announce the release of NWChem version 6.0. This version = marks a transition of NWChem to an open-source software package. The softwa= re is being released under the [Educational Community License 2.0] (ECL 2.0= ). Users can download the source code and a select set of binaries from the= new open source web site http://www.nwchem-sw.org New functionality, improvements, and bug fixes include: * Greatly improved memory management for TCE four-index transformation, CCS= D(T), CR-EOMCCSD(T), and solver for EOMCCSD * Performance and scalability improvements for TCE CCSD(T), CR-EOMCCSD(T), = and EOMCCSD * TCE based static CCSD hyperpolarizabilities * New exchange-correlation functionals available in the Gaussian DFT module * Range-separated functionals: CAM-B3LYP, LC-BLYP, LC-PBE, LC-PBE0, BNL. Th= ese functionals can also be used to perform TDDFT excited-state calculation= s * SSB-D functional * Double hybrid functionals (Semi-empirical hybrid DFT combined with pertur= bative MP2) * DFT response are now available for order 1 (linear response), single freq= uency, electric field and mixed electric-magnetic field perturbations * Greatly improved documentation for QM/MM simulations * Spin-orbit now works with direct and distributed data approaches * Plane-wave BAND module now has parallelization over k-points, AIMD, and S= pin-Orbit pseudopotentials * Plane-wave modules have improved minimizers for metallic systems and meta= dynamics capabilities * Bug fix for DISP: Empirical long-range vdW contribution * Bug fix for Hartree-Fock Exchange contributions in NMR Please let us know if have any issues accessing the new website. Best wishes, Huub __________________________________________________ Huub van Dam Scientist EMSL: Environmental Molecular Science Laboratory Pacific Northwest National Laboratory 902 Battelle Boulevard P.O. Box 999, MSIN K8-91 Richland, WA 99352 USA Tel: 509-372-6441 Fax: 509-371-6445 Hubertus.vanDam- -pnl.gov www.emsl.pnl.gov --_000_FDD09CBD8676AE40957DCDAD24E9627A01889AE16766EMAIL04pnlg_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

We are pleased to announce the release of NWChem ve= rsion 6.0. This version marks a transition of NWChem to an open-source software package. The software is being released under the [Educational Community License 2.0] (ECL 2.0). Users can download the source code and a select set= of binaries from the new open source web site http://www.nwchem-sw.org

 

New functionality, improvements, and bug fixes incl= ude:

• Greatly improved memory management for TCE four-index transformation, CCSD(T), CR-EOMCCSD(T), and solver for EOMCCSD <= o:p>

• Performance and scalability improvements fo= r TCE CCSD(T), CR-EOMCCSD(T), and EOMCCSD

• TCE based static CCSD hyperpolarizabilities=

• New exchange-correlation functionals availa= ble in the Gaussian DFT module

• Range-separ= ated functionals: CAM-B3LYP, LC-BLYP, LC-PBE, LC-PBE0, BNL. These functionals ca= n also be used to perform TDDFT excited-state calculations

• SSB-D funct= ional

• Double hybr= id functionals (Semi-empirical hybrid DFT combined with perturbative MP2)

• DFT response are now available for order 1 (linear response), single frequency, electric field and mixed electric-magn= etic field perturbations

• Greatly improved documentation for QM/MM simulations

• Spin-orbit now works with direct and distri= buted data approaches

• Plane-wave BAND module now has parallelizat= ion over k-points, AIMD, and Spin-Orbit pseudopotentials

• Plane-wave modules have improved minimizers= for metallic systems and metadynamics capabilities

• Bug fix for DISP: Empirical long-range vdW contribution

• Bug fix for Hartree-Fock Exchange contribut= ions in NMR

 

Please let us know if have any issues accessing the= new website.

 

Best wishes,

 

    Huub

 

_= _________________________________________________
Huub van = Dam
Scientist
EMSL: Environmental Molecular Science Laboratory

Pacific Northwest National Laboratory
902 Battelle Boulevard
P.O. Box 999, MSIN K8-91
Richland, WA  99352 USA
Tel:  509-372-6441
Fax: 509-371-6445
Hubertus.vanDam- -pnl.gov
www.emsl.pnl.gov

 

--_000_FDD09CBD8676AE40957DCDAD24E9627A01889AE16766EMAIL04pnlg_-- From owner-chemistry@ccl.net Wed Sep 29 17:45:00 2010 From: "case case++biomaps.rutgers.edu" To: CCL Subject: CCL: helical content time series Message-Id: <-42860-100929074516-3633-H/eBGTQl/fxXe3WUD4zPsg{}server.ccl.net> X-Original-From: case Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 29 Sep 2010 07:45:10 -0400 Mime-Version: 1.0 Sent to CCL by: case [case : biomaps.rutgers.edu] On Tue, Sep 28, 2010, Massimiliano Porrini mozz76%%gmail.com wrote: > > Does anyone know anything about an application (or code) able to calculate the > time series of the helical content of a peptide/protein by using > the trajectory obtained from a MD run? > > Specifically I have got Amber10 trajectories, but in case they could > be converted in PDB trajectories (or XYZ etc.) Amber's "ptraj" program has a "secstruct" command that analyzes secondary structure using the DSSP method. ....dac From owner-chemistry@ccl.net Wed Sep 29 19:23:00 2010 From: "Anders Sundin Anders.Sundin(_)organic.lu.se" To: CCL Subject: CCL:G: freezen dihedrals in five-membered rings Message-Id: <-42861-100929070230-17375-Rr4o5aWi4ZjsqLT0dVNTgw.:.server.ccl.net> X-Original-From: Anders Sundin Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Wed, 29 Sep 2010 13:00:31 +0200 Mime-Version: 1.0 (Apple Message framework v1081) Sent to CCL by: Anders Sundin [Anders.Sundin]|[organic.lu.se] It may be better to generate these conformations using cartesian coordinates. Number the ring atoms 1 to 5, and constrain atom 1, 2, and 3 to the x-y plane (z=0). Make constraints of atom 4 in z from -0.5 to 0.5Å, and for each such constraint, also constrain atom 5 in z from -0.5Å to 0.5Å. Repeat with atom 2, 3, 4 defining the plane, etc. -Anders Sundin On Sep 22, 2010, at 16:49 , Reynier Suard az reynier.suardiaz(a)gmail.com wrote: > > Sent to CCL by: "Reynier Suard az" [reynier.suardiaz]_[gmail.com] > Dear All > > I want to generate a lot of conformations of furanose ring (or cyclopentane?) and later partially optimize them but keeping frozen the dihedral angles. I am trying to use redundant coordinates in gaussian writing at the end of the input gaussian file the desired dihedrals to keep frozen. I am receiving an error message when i try to keep frozen more than two dihedral angles (of the ring) at the same time. > Is not possible what am I trying to do? How can I overcome this problem with gaussian? Is there any other possibility to do this kind of partial optimization in five-membered rings? Note that I can not freeze all the dihedrals using optimization in internal coordinates (opt=z-matrix with a separate input section of "constants") because of to define a z-matrix of a five-membered ring are necesary only two dihedrals, so I have to use redundants. > any comments or sugestions would be appreciatte > > thanks in advance and very best regards > > Reynier From owner-chemistry@ccl.net Wed Sep 29 19:58:00 2010 From: "Qi Chen qchen,,lilly.com" To: CCL Subject: CCL: selecting compounds for protein co-crystallization Message-Id: <-42862-100929165438-6437-ELJCi49ZK1pBIYxuhx5vDw(0)server.ccl.net> X-Original-From: "Qi Chen" Date: Wed, 29 Sep 2010 16:54:37 -0400 Sent to CCL by: "Qi Chen" [qchen\a/lilly.com] I am looking for information on what kinds of factors one should consider when selecting compounds for protein co-crystallization in general, and why. Thanks! From owner-chemistry@ccl.net Wed Sep 29 20:33:00 2010 From: "Greg Warren greg]^[eyesopen.com" To: CCL Subject: CCL: A call for papers a docking and scoring symposium at the March 2011 241st ACS National meeting in Anaheim, CA Message-Id: <-42863-100929162843-30012-uGGOcWA0vuIQE2CVqfMRag _ server.ccl.net> X-Original-From: Greg Warren Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_BB3CCF2D3D6B094D96588383620C5F3E74D965815DEXVMBX01811ex_" Date: Wed, 29 Sep 2010 13:28:36 -0700 MIME-Version: 1.0 Sent to CCL by: Greg Warren [greg .. eyesopen.com] --_000_BB3CCF2D3D6B094D96588383620C5F3E74D965815DEXVMBX01811ex_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Docking and Scoring: A Review of Docking Programs A 2004 symposium at the Philadelphia ACS meeting featured a day of overview= presentations by the developers of a large number of docking algorithms. = In an effort to find out what has changed in the last seven years we are or= ganizing a review of docking programs symposium. Instead of an overview we= are requesting that algorithm developers spend 10 minutes describing the n= ew features in and improvements to their algorithms over the last seven yea= rs. The last 15 minutes of the presentation will focus on algorithm perfor= mance for two tasks against public data sets. The first task will be bindi= ng mode prediction against the 85 structures in the Astex data set. The se= cond task will be virtual screening performance against the standard DUD d= ata set release 2 and the Wombat data. The abstract submission deadline fo= r this symposium is 11 pm Central Standard Time October 30, 2010. Please s= ee the submission instructions below. The organizers of this symposium wil= l be supplying the data to be used in this exercise shortly after the close= of abstract submission. Most Sincerely, Neysa Nevins, Georgia McGaughey and Greg Warren Submit your abstract using the following link http://abstracts.acs.org Select the 241st ACS National meeting, Anaheim, CA http://abstracts.acs.org/chem/241nm/index.php?frm=3D1 (not real clear tha= t this link will work - use with caution) Expand the programs under the COMP: Division of Computers in Chemisty (click on the +) Select Docking & Scoring: A Review of Docking Programs (Oral) Click Save You will see a list of the Division and their deadlines Click Next Enter your Name/Institution and abstract For those without an ACSid If you do not already have an ACS ID please follow these instructions: 1. Select "Registering is easy". 1. Create your username and password, and select the appropriate relation= ship to ACS. 1. When you have successfully created an ACS ID, return to the PACS homep= age and sign-in. --_000_BB3CCF2D3D6B094D96588383620C5F3E74D965815DEXVMBX01811ex_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Docking and Scoring: A Review of Docking Programs
A 2004 symposium at the Philadelphia ACS meeting featured a day of overview presentations by the developers of a large number of docking algorithms.  In an effort to find out what has changed in the last seven years we = are organizing a review of docking programs symposium.  Instead of an over= view we are requesting that algorithm developers spend 10 minutes describing the= new features in and improvements to their algorithms over the last seven years.  The last 15 minutes of the presentation will focus on algorithm performance for two tasks against public data sets.  The first task wi= ll be binding mode prediction against the 85 structures in the Astex data set.  The second task will be virtual screening performance against the standard  DUD data set release 2 and the Wombat data.  The abstra= ct submission deadline for this symposium is 11 pm Central Standard Time Octob= er 30, 2010.  Please see the submission instructions below.  The organizers of this symposium will be supplying the data to be used in this = exercise shortly after the close of abstract submission.

 

Most Sincerely,

 

Neysa Nevins, Georgia McGaughey and Greg Warren

 

 

Submit your abstract using the following link

 

= http://abstracts.acs.org

 

Select the 241st ACS National meeting, Anah= eim, CA

 

http://abstracts.acs.org/chem/241nm/index.php?frm=3D1 =   (not real clear that this link will work – use with caution)

 

Expand the programs under the COMP: Division of Comput= ers in Chemisty

(click on the +)

 

Select Docking & Scoring: A Review of Docking Prog= rams (Oral)

 

Click Save

 

You will see a list of the Division and their deadline= s

 

Click Next

 

Enter your Name/Institution and abstract

 

For those without an ACSid

 

If you do not already have an ACS ID please follow these instructions:

  1. Select “Registering is easy”.
  1. Create your username and password, and select= the appropriate relationship to ACS.
  1. When you have successfully created an ACS ID, return to the PA= CS homepage and sign-in.

 

 

 

 

--_000_BB3CCF2D3D6B094D96588383620C5F3E74D965815DEXVMBX01811ex_-- From owner-chemistry@ccl.net Wed Sep 29 22:26:00 2010 From: "rocky walden rocky.walden19(!)gmail.com" To: CCL Subject: CCL: Help needed Message-Id: <-42864-100929222348-31358-ml7wDo7lnGCCvO5H0WS/1A=-=server.ccl.net> X-Original-From: rocky walden Content-Type: multipart/alternative; boundary=0016e6d260e552b734049170c49c Date: Thu, 30 Sep 2010 07:53:42 +0530 MIME-Version: 1.0 Sent to CCL by: rocky walden [rocky.walden19{}gmail.com] --0016e6d260e552b734049170c49c Content-Type: text/plain; charset=ISO-8859-1 Hi All, I am planning to learn FORTRAN language, and i need where can i download the editors to write the code and compile it. Can any one send me a link where i can download Fortran 77/90/95 for windows XP. Regards Walden --0016e6d260e552b734049170c49c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi All,
=A0=A0 I am planning to learn FORTRAN language, and i need where= can i download the editors to write the code and compile it.
=A0=A0 Can= any one send me a link where i can download Fortran 77/90/95 for windows X= P.


Regards
Walden
--0016e6d260e552b734049170c49c--