From owner-chemistry@ccl.net Thu Aug 13 02:04:01 2009 From: "Kshatresh Dutta Dubey kshatresh(!)gmail.com" To: CCL Subject: CCL: Query about Scoring functions Message-Id: <-39980-090813015319-3565-cvVUcXUZO/34WaMbA+9/TQ#,#server.ccl.net> X-Original-From: Kshatresh Dutta Dubey Content-Type: multipart/alternative; boundary=00151773e71ea6ceab0470fe834f Date: Thu, 13 Aug 2009 10:08:59 +0530 MIME-Version: 1.0 Sent to CCL by: Kshatresh Dutta Dubey [kshatresh.:.gmail.com] --00151773e71ea6ceab0470fe834f Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi, If G_score corresponds to Glide docking then you should consider negative value. If you have two or more negative values then the best score will be of highest negative value. Kshatresh Dutta Dubey On Wed, Aug 12, 2009 at 10:03 PM, Need47 need47%a%gmail.com < owner-chemistry-.-ccl.net> wrote: > HI, Sobia > > If your scores are from SYBYL, consider the negative ones. > > Jay > > On Tue, Aug 11, 2009 at 9:09 AM, sobia ahsan halim sobia_halim-x-yahoo.com > > wrote: > >> >> Sent to CCL by: "sobia ahsan halim" [sobia_halim|yahoo.com] >> >> Dear All >> Hi >> >> I need to know some thing about G_score, D_score, PMF and Chemscore. These >> scoring functions gives positive and negative values. Whether we should >> consider their positive value or negative one. >> Thanks in advance >> >> Regards, >> Sobia.>> E-mail to subscribers: CHEMISTRY|,|ccl.net or >> use:>> >> E-mail to administrators: CHEMISTRY-REQUEST|,|ccl.netor use>> >> >> >> > --00151773e71ea6ceab0470fe834f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,

=A0If G_score corresponds to Glide docking then you should consi= der negative value. If you have two or more negative values then the best s= core will be of highest negative value.

Kshatresh Dutta Dubey
On Wed, Aug 12, 2009 at 10:03 PM, Need47 need47%= a%gmail.com <owner-chemistry-.-ccl.net> = wrote:
HI, Sobia

= If your scores are from SYBYL, consider the negative ones.

Jay
On Tue, Aug 11, 2009 at 9:09 AM, sobia ahsan hal= im sobia_halim= -x-yahoo.com <owner-chemistry|,|ccl.net> wro= te:
<= div>
Sent to CCL by: "sobia ahsan halim" [sobia_halim|yahoo.com]

Dear All
Hi

I need to know some thing about G_score, D_score, PMF and Chemscore. These = scoring functions gives positive and negative values. Whether we should con= sider their positive value or negative one.
Thanks in advance

Regards,
Sobia.



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--00151773e71ea6ceab0470fe834f-- From owner-chemistry@ccl.net Thu Aug 13 09:18:00 2009 From: "John McKelvey jmmckel(!)gmail.com" To: CCL Subject: CCL: ZINDO compilation saga continues Message-Id: <-39981-090813091126-15703-lr/tBxSHL0tZUUqLF7Jzfw**server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=001636ed67765bae880471058f3c Date: Thu, 13 Aug 2009 09:03:20 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel++gmail.com] --001636ed67765bae880471058f3c Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Folk, Kevin Gilbert has gotten a long way in compiling ZINDO with GFortran/GCC om a MAC(i.e. Linux). I downloaded the Windows version, but GCC complains about no stdio.h !!!! Most Bazaar!!! Anyone tried Gfort/GCC on Windows and gotten GCC to work? Thanks! John -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel|gmail.com --001636ed67765bae880471058f3c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Folk,

Kevin Gilbert has gotten a long way in compiling ZINDO with GF= ortran/GCC om a MAC(i.e. Linux).=A0 I downloaded the Windows version, but G= CC complains about no stdio.h !!!!=A0 Most Bazaar!!!=A0 Anyone tried Gfort/= GCC on Windows and gotten GCC to work?

Thanks!

John

--
John McKelvey
10819 = Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel|gmail.com
--001636ed67765bae880471058f3c-- From owner-chemistry@ccl.net Thu Aug 13 09:53:01 2009 From: "Len Villamin Lim murdockdx(~)yahoo.com" To: CCL Subject: CCL: Split peak in spectra of water Message-Id: <-39982-090813053521-13274-Q/A/JbvyybFHtaAGmt45jg*_*server.ccl.net> X-Original-From: "Len Villamin Lim" Date: Thu, 13 Aug 2009 05:35:16 -0400 Sent to CCL by: "Len Villamin Lim" [murdockdx_+_yahoo.com] I'm working on computer simulations of metal ions in solution using a hybrid QM/MM framework. One thing that interested me is the IR spectra of water molecules near the ion and I've tried to generate spectra via FT of autocorrelation functions of the normal modes. I'm relatively new to the idea, but I was able to get (more or less) sensible values for the frequencies (e.g. ~3900/cm for H2O symmetric stretch). It puzzles me though that for one particular ion (Sn(II)) I get small side peaks for the stretching frequencies for 1st and 2nd shell water molecules. Can someone help me figure it out? (is there some known mistakes that lead to this? or is there likely to be some vibrational coupling involved?). I'd appreciate the help. Len Herald Lim len.lim##student.uibk.ac.at University of Innsbruck Innrain 52a A-6020 Innsbruck From owner-chemistry@ccl.net Thu Aug 13 11:52:00 2009 From: "Basma Ghazal basmaghazal() ymail.com" To: CCL Subject: CCL: aproblem in docking Message-Id: <-39983-090811184034-7836-R9IKgfhLXSVbFefFAbb1WA:_:server.ccl.net> X-Original-From: Basma Ghazal Content-Type: multipart/alternative; boundary="0-396412838-1250030421=:4700" Date: Tue, 11 Aug 2009 15:40:21 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Basma Ghazal [basmaghazal(-)ymail.com] --0-396412838-1250030421=:4700 Content-Type: text/plain; charset=us-ascii Dear All: After making docking by autodock and Vegazz and have the minimum energy I found amissing residue in my Pdb structure If some one have any explanation please seand it Thanks --0-396412838-1250030421=:4700 Content-Type: text/html; charset=us-ascii
Dear All:
After making docking by autodock and Vegazz and have the minimum energy I found amissing residue in my Pdb structure If some one have any explanation please seand it
Thanks

--0-396412838-1250030421=:4700-- From owner-chemistry@ccl.net Thu Aug 13 12:27:00 2009 From: "Reinaldo Pis Diez reinaldo.pisdiez-#-gmail.com" To: CCL Subject: CCL: ZINDO compilation saga continues Message-Id: <-39984-090813112911-13985-69R5uKodRoFFeUDvsZByfw[#]server.ccl.net> X-Original-From: Reinaldo Pis Diez Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 13 Aug 2009 11:22:33 -0300 MIME-Version: 1.0 Sent to CCL by: Reinaldo Pis Diez [reinaldo.pisdiez a gmail.com] Dear John, The most decent manner to compile programs under MSWindows using free compilers like gfortran and gcc is installing cygwin firstly. It comes with gcc, gfortran must be installed separately. Regards, Reinaldo John McKelvey jmmckel(!)gmail.com escribió: > Folk, > > Kevin Gilbert has gotten a long way in compiling ZINDO with GFortran/GCC > om a MAC(i.e. Linux). I downloaded the Windows version, but GCC > complains about no stdio.h !!!! Most Bazaar!!! Anyone tried Gfort/GCC > on Windows and gotten GCC to work? > > Thanks! > > John > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel~~gmail.com From owner-chemistry@ccl.net Thu Aug 13 14:02:00 2009 From: "amit dong dongamit123~!~gmail.com" To: CCL Subject: CCL: heavy atoms Message-Id: <-39985-090813140031-14317-Jk4LJqnQ/mUw6F1yBxONZw(0)server.ccl.net> X-Original-From: amit dong Content-Type: multipart/alternative; boundary=00163662e6e17fc434047109b523 Date: Thu, 13 Aug 2009 13:00:20 -0500 MIME-Version: 1.0 Sent to CCL by: amit dong [dongamit123*o*gmail.com] --00163662e6e17fc434047109b523 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi, I need to search for analogs of a compound in a database. Is there any tool that I can use for this purpose. Thanks AD --00163662e6e17fc434047109b523 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi,

I need to search for analogs of a compound in a database. Is there any tool that I can use for this purpose.

Thanks
AD


--00163662e6e17fc434047109b523-- From owner-chemistry@ccl.net Thu Aug 13 14:37:01 2009 From: "amit dong dongamit123~~gmail.com" To: CCL Subject: CCL: analog search Message-Id: <-39986-090813140224-14618-1M5E3iT08RCUhza1A/Rirw-$-server.ccl.net> X-Original-From: amit dong Content-Type: multipart/alternative; boundary=0016e645a3fa286563047109bc8c Date: Thu, 13 Aug 2009 13:02:12 -0500 MIME-Version: 1.0 Sent to CCL by: amit dong [dongamit123=-=gmail.com] --0016e645a3fa286563047109bc8c Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi, I need to search for analogs of a compound in a database. Is there any tool that I can use for this purpose. Thanks AD --0016e645a3fa286563047109bc8c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit 
Hi,

I need to search for analogs of a compound in a database. Is there any tool
that I can use for this purpose.

Thanks
AD
--0016e645a3fa286563047109bc8c-- From owner-chemistry@ccl.net Thu Aug 13 15:19:00 2009 From: "Dalila Hammoutene Dalila.Hammoutene~!~univ-mlv.fr" To: CCL Subject: CCL: Frequency-dependent dielectric constant Message-Id: <-39987-090813143114-28654-Bx7LHZKrYplRh97PuYnusA.@.server.ccl.net> X-Original-From: "Dalila Hammoutene" Date: Thu, 13 Aug 2009 14:31:10 -0400 Sent to CCL by: "Dalila Hammoutene" [Dalila.Hammoutene|a|univ-mlv.fr] Dear CCLers How can one compute the frequency-dependent dielectric constant of a small organic molecule? Perhaps via frequency-dependent polarizability? So, which correct formula should be used? Thanks in advance. Dalila. Dalila.Hammoutene a univ-mlv.fr Laboratory of Thermodynamics and Molecular Modelisation, Faculty of Chemistry, USTHB University, BP32 El Alia 16111 Algiers, Algeria. From owner-chemistry@ccl.net Thu Aug 13 15:47:00 2009 From: "Esteban Gabriel Vega Hissi egvega . gmail.com" To: CCL Subject: CCL: aproblem in docking Message-Id: <-39988-090813151148-24465-w9w9wAyG2ckNsbf69kEQBQ!^!server.ccl.net> X-Original-From: Esteban Gabriel Vega Hissi Content-Type: multipart/alternative; boundary=0016364c7b990f52dc04710ab425 Date: Fri, 14 Aug 2009 15:11:31 +2000 MIME-Version: 1.0 Sent to CCL by: Esteban Gabriel Vega Hissi [egvega .. gmail.com] --0016364c7b990f52dc04710ab425 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi, I've used Autodock without the problem you report here. Check carfully the original pdb and the pdbqt. You can also try in Autodock Mailing List here: http://mgldev.scripps.edu/mailman/listinfo/autodock Best. Esteban G. Vega Hissi UNSL Argentina 2009/8/12 Basma Ghazal basmaghazal() ymail.com > Dear All: > After making docking by autodock and Vegazz and have the minimum energy I > found amissing residue in my Pdb structure If some one have any explanation > please seand it > Thanks > > --0016364c7b990f52dc04710ab425 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,
I've used Autodock without the problem you report here.
Chec= k carfully the original pdb and the pdbqt.

You can also try in Autod= ock Mailing List here:
http://mgldev.scripps.edu/mailman/listinfo= /autodock

Best.

Esteban G. Vega Hissi
UNSL
Argentina


--0016364c7b990f52dc04710ab425-- From owner-chemistry@ccl.net Thu Aug 13 16:22:00 2009 From: "Andrew Orry andy()molsoft.com" To: CCL Subject: CCL: Protein Structure and Drug Discovery Workshop - October 1st - 2nd 2009 Message-Id: <-39989-090813141224-18808-VBCIwZFl8bdCgjoAtKMZsA.@.server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Thu, 13 Aug 2009 10:06:04 -0700 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy\a/molsoft.com] **MolSoft ICM Workshop: "Protein Structure and Drug Discovery" October 1st to 2nd 2009 La Jolla, CA.** Please see the following invitation to attend MolSoft's ( www.molsoft.com ) "Protein Structure and Drug Design Workshop" on October 1st to 2nd 2009 in La Jolla, California USA. Please see www.molsoft.com/training.html for more information and a registration form. Our workshops are suitable for chemists and biologists who would like to learn more about computational drug discovery and bioinformatics. No prior knowledge in this field is required to participate. The workshop is presented by Prof. Ruben Abagyan (University of California San Diego) and Dr. Maxim Totrov (MolSoft). Price: $360 (before September 1st) $400 (after September 1st) The workshops will consist of lectures, demonstrations, and "hands-on" computational experiments and will cover the following topics: - Molecular Graphics and Displaying Interactive Molecules in PowerPoint and the Web see: http://www.molsoft.com/activeicm.html . - Sequence and Protein Structure Analysis. - Protein Modeling and Simulations. - Structure Validation and Optimization. - Ligand Binding Site Prediction. - Small Molecule Docking and Virtual Ligand Screening. - Structure-based development of target-specific compound libraries - Cheminformatics, Chemical Clustering, Searching, Superposition etc... - QSAR, Machine Learning - Protein-Protein Docking We will demonstrate and train you in the use of many of our new developments in computational chemistry and biology including: - 3D Ligand Editor - design and optimize ligands interactively see http://www.molsoft.com/gui/ligand-editor.html - Markush Library Docking - Multiple Receptor Docking (A method to incorporate receptor flexibility) - Automated model building into electron density - Atomic property field chemical superposition - Fast machine learning tools for QSAR - Pharmacophore drawing and searching - Compound library enumeration tools - Screen-grabbing molecular movie making "The objective of this training workshop is to help chemists and biologists solve challenging problems in the area of drug discovery by efficient use of the science and technology present in ICM molecular modeling tools." Prof. Ruben Abagyan (University of California San Diego and Co-Founder of Molsoft LLC) Please see our website at www.molsoft.com for more details or E mail andy..@..molsoft.com or call (858) 625 2000 ext.108. Please join the ICM Discussion Forum: http://groups.google.com/group/molsoft-icm-forum Latest News: http://www.molsoft.com/news.html MolSoft is a La Jolla based company that is a primary source of new breakthrough technologies in computational chemistry and biology. Molsoft is committed to solving intellectually challenging problems in drug discovery and computational biology. From owner-chemistry@ccl.net Thu Aug 13 16:58:01 2009 From: "Morad M El-Hendawy M80elhendawy],[yahoo.com" To: CCL Subject: CCL: Software for calculation DOS and PDOS Message-Id: <-39990-090813161328-12462-Mm4koWqqfH6NHxtuZBnRzQ a server.ccl.net> X-Original-From: "Morad M El-Hendawy" Date: Thu, 13 Aug 2009 16:13:24 -0400 Sent to CCL by: "Morad M El-Hendawy" [M80elhendawy::yahoo.com] Hi every body, I wonder if anyone tell me about a reputed software for calculating Density Of State (DOS) and Partial Density Of State (PDOS) My regards Morad El-Hendawy Ireland From owner-chemistry@ccl.net Thu Aug 13 17:32:01 2009 From: "Zdenek Chval chval]~[jcu.cz" To: CCL Subject: CCL:G: Fixing bond length in Gaussian. Message-Id: <-39991-090812183014-14214-1e/eNgEBYWZUY6WgOvrDVQ(a)server.ccl.net> X-Original-From: Zdenek Chval Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Wed, 12 Aug 2009 23:16:15 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Zdenek Chval [chval++jcu.cz] It can be achieved by more ways. If you use cartesian coordinates then after blank line write numbers of fixed atoms and wildcart "F". It should be used with "opt=ModRedundant" keyword. e.g. for the following hypothetical CO2 molecule distance between atoms 1 and 2 can be fixed by: 0 1 C 0.0 0.0 0.0 O 1.2 0.0 0.0 O -1.2 0.0 0.0 1 2 F Best regards, Zdenek Chval On Wed, 12 Aug 2009, Rashid, Ali ARashid],[ppg.com wrote: > I was hoping that someone could help me with a small problem that I am having. > > I am a new Gaussian user and I would like to know how to constrain a bond length in a molecule. > > I have access to gauss view and materials studio. > > Thank you in advance. > > > > > > > =========================== > Ali N. Rashid PhD. > Senior Research Scientist > > PPG Industries Inc. > Glass Business and Discovery Center > 400 Guys Run Road > Cheswick, PA 15024 USA > > Telephone:(412) 820-8511 > Fax: (412) 820-8515 > arashid|a|ppg.com > =========================== > > From owner-chemistry@ccl.net Thu Aug 13 18:14:01 2009 From: "Mihaly Mezei Mihaly.Mezei*o*mssm.edu" To: CCL Subject: CCL: analog search Message-Id: <-39992-090813171330-31111-Z5C0ryyueHrFojM1tx8Jrg++server.ccl.net> X-Original-From: Mihaly Mezei Content-disposition: inline Content-language: en Content-transfer-encoding: 7BIT Content-type: text/plain; charset=us-ascii Date: Thu, 13 Aug 2009 15:48:59 -0400 MIME-version: 1.0 Sent to CCL by: Mihaly Mezei [Mihaly.Mezei^-^mssm.edu] ----- Original Message ----- > From: "amit dong dongamit123~~gmail.com" Date: Thursday, August 13, 2009 2:02 pm Subject: CCL: analog search > I need to search for analogs of a compound in a database. Is there > any tool that I can use for this purpose. You can try the ZINC database: >http://zinc.docking.org/ It has a structre search facility. Mihaly Mezei Department of Structural and Chemical Biology, Mount Sinai School of Medicine, NYU Voice: (212) 659-5475 Fax: (212) 849-2456 WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632 WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei WWW (Department): http://atlas.physbio.mssm.edu From owner-chemistry@ccl.net Thu Aug 13 22:56:01 2009 From: "Konrad Hinsen hinsen^-^cnrs-orleans.fr" To: CCL Subject: CCL: Frequency-dependent dielectric constant Message-Id: <-39993-090813223533-21639-n0OlqXn2RMUKM7DSWvAiIg]_[server.ccl.net> X-Original-From: "Konrad Hinsen" Date: Thu, 13 Aug 2009 22:35:29 -0400 Sent to CCL by: "Konrad Hinsen" [hinsen%%cnrs-orleans.fr] "Dalila Hammoutene" [Dalila.Hammoutene|a|univ-mlv.fr] writes: > How can one compute the frequency-dependent dielectric constant of a small > organic molecule? Perhaps via frequency-dependent polarizability? So, which > correct formula should be used? The dielectric constant is a bulk property that depends not only on an individual molecule, but also on its interactions with other molecules. To calculate it, you would need to perform a Molecular Dynamics simulation of the substance of interest at the right temperature and pressure. -- --------------------------------------------------------------------- Konrad Hinsen Centre de Biophysique Molculaire, CNRS Orlans Synchrotron Soleil - Division Expriences Saint Aubin - BP 48 91192 Gif sur Yvette Cedex, France Tel. +33-1 69 35 97 15 E-Mail: hinsen at cnrs-orleans.fr ---------------------------------------------------------------------