From owner-chemistry@ccl.net Wed Sep 9 02:38:01 2009 From: "Marcel Swart marcel.swart**icrea.es" To: CCL Subject: CCL:G: Atoms repulsion calculation Message-Id: <-40197-090909021436-29982-tx7+fiNAb1ZSnegnnj7hZA]![server.ccl.net> X-Original-From: Marcel Swart Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Wed, 9 Sep 2009 08:10:01 +0200 MIME-Version: 1.0 Sent to CCL by: Marcel Swart [marcel.swart|a|icrea.es] The energy decomposition analysis in ADF might help in this case, just as e.g. shown in: F. M. Bickelhaupt, E. J. Baerends The Case for Steric Repulsion Causing the Staggered Conformation of Ethane Angew. Chem. 2003, 115, 4315-4320. Angew. Chem. Int. Ed. 2003, 42, 4183-4188 J. Poater, M. Sol=E0, F. M. Bickelhaupt Hydrogen?Hydrogen Bonding in Planar Biphenyl, Predicted by =20 Atoms-In-Molecules Theory, Does Not Exist Chem. Eur. J. 2006, 12, 2889-2895 and many other papers related to these. Quoting "Henry Martinez hmartine- -gmail.com" : > > Sent to CCL by: "Henry Martinez" [hmartine.:.gmail.com] > Hi, I am using Gaussian 03, and I would like to know if there is =20 > anyway I would be able to know if there is any repulsion interaction =20 > between two atoms of the same molecule that are close to each =20 > other. For being more specific, there is an internal cyclization =20 > reaction. The atom who attacks can do it from one angle or another, =20 > however after calculating the Transition state the angle of the =20 > attacker makes me think that there might be a repulsion =20 > interaction. How can I know this? > Thanks a lot > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D dr. Marcel Swart ICREA Research Professor at Institut de Qu=EDmica Computacional Universitat de Girona Parc Cient=EDfic i Tecnol=F2gic Edifici Jaume Casademont (despatx A-27) Pic de Peguera 15 17003 Girona Catalunya (Spain) tel +34-972-183240 fax +34-972-183241 e-mail marcel.swart ~ icrea.es marcel.swart ~ udg.edu web http://www.icrea.cat/Web/ScientificForm.aspx?key=3D372 http://iqc.udg.edu/~marcel =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D From owner-chemistry@ccl.net Wed Sep 9 08:46:01 2009 From: "arslan ali arslanali1986,,gmail.com" To: CCL Subject: CCL: mopac for mass fragments Message-Id: <-40198-090909004952-19698-E6crDHqgNHE/cWGbsuUmzQ_+_server.ccl.net> X-Original-From: "arslan ali" Date: Wed, 9 Sep 2009 00:49:48 -0400 Sent to CCL by: "arslan ali" [arslanali1986()gmail.com] hi i am a biggner for Mopac use in Mass spectrometry of organic molecules. can any body please give me tutorial or sop regarding MOPAC use to calculate different energies like SPE, ZPE, transition state etc prayers and regards Arslan From owner-chemistry@ccl.net Wed Sep 9 10:03:01 2009 From: "=?gb2312?B?wO7H5dDx?= liqx.:.cqupt.edu.cn" To: CCL Subject: CCL: M05 and M05-2X density functionals Message-Id: <-40199-090908085224-4546-CAfKjtVpmJwveByaswjyhg**server.ccl.net> X-Original-From: "=?gb2312?B?wO7H5dDx?=" Content-Type: multipart/alternative; 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While building a model for a set of compounds, how does one make the choice of molecular descriptors. As more than thousands of them can be calculated, it looks good to use all of them. But will it make sense? What methods/packages can be used in deciding the right choice of descriptors? Can you please post relevant software that can be used here.. Thanks Sangeetha. From owner-chemistry@ccl.net Wed Sep 9 11:39:00 2009 From: "Basma Ghazal basmaghazal_+_ymail.com" To: CCL Subject: CCL: abroblem with arguslab Message-Id: <-40201-090909113737-25905-ALyIErVk+R1PnUcRnOFAgw{=}server.ccl.net> X-Original-From: Basma Ghazal Content-Type: multipart/alternative; boundary="0-2127587352-1252510645=:44811" Date: Wed, 9 Sep 2009 08:37:25 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Basma Ghazal [basmaghazal%ymail.com] --0-2127587352-1252510645=:44811 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi, I'am=A0a newer user for=A0ArgusLab 4.0.1=A0 I have some=A0questions include : 1. the RMSD=A0value is different=A0from in the tutorial examples. =A02.=A0I need=A0=A0to make the results more real. =A0 3. they said that ( =D8=A0=A0=A0=A0 When a Ligand group is docking, it will ignore all other at= oms that belong to any other Ligand groups that are present.=A0 Thus, you c= an dock multiple ligands into the same structure and see the final results = overlaid on each other.=A0 However, if you forget to create a Ligand group = of a molecule that already occupies the binding site, it will adversely aff= ect the docking results.) .=20 If that mean that I have to leave aligand X-ray=A0at the binding site ,Wher= e does my ligand will bind? =A0Thanks =0A=0A=0A --0-2127587352-1252510645=:44811 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi,
I'am a newe= r user for ArgusLab 4.0.1 
= I have some questions include :
1. the RMSD value is differen= t from in the tutorial examples.
 2.&= nbsp;I need  to make the results more real.
  3. they said that (

= =D8     When a Ligand group is docking, it = will ignore all other atoms that belong to any other Ligand groups that are= present.  Thus, you can dock multiple ligands into the same structure= and see the final results overlaid on each other.  However, if you fo= rget to create a Ligand group of a molecule that already occupies the bindi= ng site, it will adversely affect the docking results.) .

<= STRONG>If that mean that I have to leave aligand X-ray = at the binding site ,Where does my ligand will bind?

 Thanks

=0A=0A --0-2127587352-1252510645=:44811-- From owner-chemistry@ccl.net Wed Sep 9 12:14:01 2009 From: "Rajarshi Guha rajarshi.guha+*+gmail.com" To: CCL Subject: CCL: Molecular descriptor selection Message-Id: <-40202-090909114245-30570-3FvgNqjGV8kYCqwSpvU7Tg#server.ccl.net> X-Original-From: Rajarshi Guha Content-Type: multipart/alternative; boundary=000e0cd6c854bbbf7e047326d3fd Date: Wed, 9 Sep 2009 11:35:05 -0400 MIME-Version: 1.0 Sent to CCL by: Rajarshi Guha [rajarshi.guha/a\gmail.com] --000e0cd6c854bbbf7e047326d3fd Content-Type: text/plain; charset=ISO-8859-1 On Wed, Sep 9, 2009 at 8:46 AM, Sangeetha Subramaniam srdshigella .. gmail.com wrote: > > Sent to CCL by: "Sangeetha Subramaniam" [srdshigella],[gmail.com] > > While building a model for a set of compounds, how does one make the choice > of molecular descriptors. As more than thousands of them can be calculated, > it looks good to use all of them. But will it make sense? > > What methods/packages can be used in deciding the right choice of > descriptors? > This is the problem of feature selection and there is detailed statistical literature on this topic. In addition there are a number of papers in JCIM describing a variety of methods to perform this task. The simplest way is to use prior knowledge (and precedent) to manually select descriptors. Automated methods include genetic algorithms, simulated annealing, stepwise regression (not a great idea) and so on. R is a good environement in which to experiment with a variety of methods -- Rajarshi Guha NIH Chemical Genomics Center --000e0cd6c854bbbf7e047326d3fd Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

On Wed, Sep 9, 2009 at 8:46 AM, Sangeeth= a Subramaniam srdshigella .. gmail.com <owner-chemist= ry|,|ccl.net> wrote:

Sent to CCL by: "Sangeetha =A0Subramaniam" [srdshigella],[gmail.com]

While building a model for a set of compounds, how does one make the choice= of molecular descriptors. As more than thousands of them can be calculated= , it looks good to use all of them. But will it make sense?

What methods/packages can be used in deciding the right choice of descripto= rs?

This is the problem of feature selection and t= here is detailed statistical literature on this topic. In addition there ar= e a number of papers in JCIM describing a variety of methods to perform thi= s task. The simplest way is to use prior knowledge (and precedent) to manua= lly select descriptors. Automated methods include genetic algorithms, simul= ated annealing, stepwise regression (not a great idea) and so on.

R is a good environement in which to experiment with a variety of metho= ds


--
Rajarshi Guha
NIH Chemic= al Genomics Center
--000e0cd6c854bbbf7e047326d3fd-- From owner-chemistry@ccl.net Wed Sep 9 17:01:00 2009 From: "Isaac B Bersuker bersuker_._cm.utexas.edu" To: CCL Subject: CCL: Molecular descriptor selection Message-Id: <-40203-090909141843-14197-gb9EHjL0WCtMD5NZ66Sw1w~~server.ccl.net> X-Original-From: Isaac B Bersuker Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8 Date: Wed, 9 Sep 2009 17:40:56 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: Isaac B Bersuker [bersuker(-)cm.utexas.edu] One possibility (rigorous, but not easy) is to employ QSAR without arbitrary descriptors, see J. Comp.-Aided Mol. Des. 22, N 6-7, 423-430 (2008). Dr. Isaac B. Bersuker Institute for Theoretical Chemistry The University of Texas at Austin Chem & Biochem Department 1 University Station A5300 Austin, TX 78712-0165 Phone: (512) 471-4671; Fax: (512) 471-8696 E-mail: bersuker- -cm.utexas.edu http://www.cm.utexas.edu/isaac_bersuker ----- Original Message ----- > From: "Sangeetha Subramaniam srdshigella .. gmail.com" To: "Isaac B. Bersuker" Sent: Wednesday, September 9, 2009 7:46:35 AM GMT -06:00 US/Canada Central Subject: CCL: Molecular descriptor selection Sent to CCL by: "Sangeetha Subramaniam" [srdshigella],[gmail.com] Hello everyone, I have a query and would be glad to hear all your suggestions. While building a model for a set of compounds, how does one make the choice of molecular descriptors. As more than thousands of them can be calculated, it looks good to use all of them. But will it make sense? What methods/packages can be used in deciding the right choice of descriptors? Can you please post relevant software that can be used here.. Thanks Sangeetha.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt