From owner-chemistry@ccl.net Mon Jan 26 00:24:01 2009 From: "Mohammad ghasemnejad esfahlani gesfahlan*azaruniv.edu" To: CCL Subject: CCL: A question about force field parametrization Message-Id: <-38506-090125041927-22949-eJ9s/Mp8/sWLLLm7VN7KNw _ server.ccl.net> X-Original-From: "Mohammad ghasemnejad esfahlani" Content-Type: multipart/alternative; boundary="_0125-1213-01-PART-BREAK" Date: Sun, 25 Jan 2009 12:13:01 +0330 MIME-Version: 1.0 Sent to CCL by: "Mohammad ghasemnejad esfahlani" [gesfahlan^_^azaruniv.edu] --_0125-1213-01-PART-BREAK Content-Type: text/plain; charset=us-ascii Hi, Hope will find all in good health.I am Msc student in Azarbayjan university of Tarbiyat Moallem. I am working on the force field parameterization of carbon nanotubes in various conditions .I can not calculate the torsion ,angle constant or energy and many other parameters .I found in some article that this constant or energy directly obtained from Experimental or Quantum mechanical calculatins.But I wish to obtain these parameters from quantum mechanical calculations .Is true way? Which software suitable? Please kindly help me for solve these problems. > Best wishes. --_0125-1213-01-PART-BREAK Content-Type: text/html; charset=us-ascii
Hi, Hope will find all in good health.I am Msc student in
Azarbayjan university of Tarbiyat Moallem. I am working on the force
field
parameterization of carbon nanotubes in various conditions .I can not
calculate the torsion ,angle constant or energy and many other
parameters .I found in some article that this constant or energy directly
obtained from Experimental or Quantum mechanical calculatins.But I wish
to
obtain these parameters from quantum mechanical calculations .Is true
way?
Which software suitable? Please kindly help me for solve these problems.
> Best wishes.

 
 --_0125-1213-01-PART-BREAK-- From owner-chemistry@ccl.net Mon Jan 26 08:28:01 2009 From: "Carlos Lagos A. carlos*o*cbuc.cl" To: CCL Subject: CCL: Toxophores database Message-Id: <-38507-090126081427-18266-NNcuKTMm5Hn6Q/U/s6rWsg * server.ccl.net> X-Original-From: "Carlos Lagos A." Content-Type: multipart/alternative; boundary="----=_NextPart_000_000A_01C97F9A.5DBC6A50" Date: Mon, 26 Jan 2009 09:42:13 -0400 MIME-Version: 1.0 Sent to CCL by: "Carlos Lagos A." [carlos{}cbuc.cl] This is a multi-part message in MIME format. ------=_NextPart_000_000A_01C97F9A.5DBC6A50 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit You can try also the free web version of ADME/Tox boxes (http://www.pharma-algorithms.com/webboxes/) were you may paste the smile of your molecule and have a prediction of genotoxicity and health effects. Batch calculation are available only on the commercial version. QF Carlos Lagos A. Centre for Bioinformatics, Faculty of Biological Sciences Medicinal Chemistry Laboratory, Faculty of Chemistry P. Universidad Catolica de Chile I Portugal # 49, Zocalo ZIP 8330025 I Santiago - Chile Phone: + 56 2 6862269 I http://www.cbuc.cl _____ De: owner-chemistry+carlos==cbuc.cl(0)ccl.net [mailto:owner-chemistry+carlos==cbuc.cl(0)ccl.net] En nombre de Grace Y Tier Grace.Y.Tier .. usa.dupont.com Enviado el: Viernes, 23 de Enero de 2009 16:01 Para: Lagos, Carlos F Asunto: CCL: Toxophores database MCASE is another expert system that contains toxicophores but this is commercial. The only one that comes to mind that is not commerically available is the OECD Toolbox. Within the Toolbox you will find a number of profiling tools e.g. Verhaar scheme, Protein binding, DNA binding. The DNA binding tool identifies structural features that are indicative of genotoxic action. see http://www.oecd.org/document/23/0,3343,en_2649_34379_33957015_1_1_1_1,00.htm l#Download_the__QSARs_Application_Toolbox for more details on how to download and install. There is a wealth of training material available for the Toolbox. Much of that is aimed at users who wish to apply the Toolbox for the development and evaluation of chemical categories and read-across. The profiling tools are one means to evaluate the "similarity with respect to a chemical mechanism of action". Grace "Chupakhin Vladimir chupvl|*|gmail.com" Sent by: owner-chemistry+grace.y.tier==usa.dupont.com^ccl.net 01/23/2009 02:25 PM Please respond to "CCL Subscribers" To Grace Y Tier/AE/DuPont^DuPont cc Subject CCL: Toxophores database Dear CCL subscribers, I am looking for the database of the toxophores (mutagens, teratogenes, etc) - open or academically avaliable. The only one I have found is Benigni-Bossa rulebase implemented in ToxTree software. Also there is a DEREK software from LHASA that also have rule-based toxophores but it's commercial. Are there anything else except above mentioned? Vladimir Chupakhin, Moscow State University This communication is for use by the intended recipient and contains information that may be Privileged, confidential or copyrighted under applicable law. If you are not the intended recipient, you are hereby formally notified that any use, copying or distribution of this e-mail, in whole or in part, is strictly prohibited. Please notify the sender by return e-mail and delete this e-mail from your system. Unless explicitly and conspicuously designated as "E-Contract Intended", this e-mail does not constitute a contract offer, a contract amendment, or an acceptance of a contract offer. This e-mail does not constitute a consent to the use of sender's contact information for direct marketing purposes or for transfers of data to third parties. Francais Deutsch Italiano Espanol Portugues Japanese Chinese Korean http://www.DuPont.com/corp/email_disclaimer.html ------=_NextPart_000_000A_01C97F9A.5DBC6A50 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

You can try also = the free web version of ADME/Tox boxes (http://www.pharma-alg= orithms.com/webboxes/) were you may paste the smile of your molecule and have a prediction of genotoxicity and health effects. Batch calculation are available only on = the commercial version.

 =

QF Carlos Lagos A. =
Centre for Bioinformatics, Faculty of Biological Sciences
Medicinal Chemistry Laboratory, Faculty of Chemistry
P. Universidad Catolica de Chile I Portugal # 49, Zocalo
ZIP 8330025 = I Santiago – Chile
Phone: + 56 2 6862269 = I http://www.cbuc.cl<= /font>

De: owner-chemistry+carlos=3D=3Dcbuc.cl(0)ccl.net [mailto:owner-chemistry+carlos=3D=3Dcbuc.cl(0)ccl.net] En nombre de Grace Y Tier Grace.Y.Tier .. = usa.dupont.com
Enviado el: Viernes, = 23 de = Enero de 2009 16:01
Para: Lagos, Carlos F =
Asunto: CCL: Toxophores = database

 


MCASE is another expert system that contains toxicophores but this is commercial. The only one that comes to mind = that is not commerically available is the OECD Toolbox. Within the Toolbox you = will find a number of profiling tools e.g. Verhaar scheme, Protein binding, = DNA binding. The DNA binding tool identifies structural features that are indicative of genotoxic action.

see http://www.oecd.org/document/23/0,3343,en_2649_34379_33957015_1_1_1_1,00.= html#Download_the__QSARs_Application_Toolbox for more details on how to download and install. There is a wealth of = training material available for the Toolbox. Much of that is aimed at users who = wish to apply the Toolbox for the development and evaluation of chemical = categories and read-across. The profiling tools are one means to evaluate the = "similarity with respect to a chemical mechanism of action".


Grace



"Chupakhin = Vladimir chupvl|*|gmail.com" = <owner-chemistry^ccl.net>
Sent by: = owner-chemistry+grace.y.tier=3D=3Dusa.dupont.com^ccl.net =

01/23/2009= 02:25 PM

Please respond to
"CCL Subscribers" = <chemistry^ccl.net>

To

Grace Y = Tier/AE/DuPont^DuPont

cc

 

Subject

CCL: Toxophores = database

 

 

 




Dear CCL subscribers,
 
I am looking for the database of the toxophores (mutagens, teratogenes, = etc) - open or academically avaliable. The only one I have found is  Benigni-Bossa rulebase implemented in ToxTree = software. Also there is a DEREK software from LHASA that also have rule-based = toxophores but it's commercial.
 
Are there anything else except above mentioned?
 
 
Vladimir Chupakhin,
Moscow State University 

 
This =
communication is for use by the intended recipient and =
contains
information that may be Privileged, =
confidential or copyrighted =
under
applicable law. If you are not the intended =
recipient, you are hereby
formally =
notified that any use, copying or distribution of this =
e-mail,
in whole =
or in part, is strictly prohibited. Please notify the sender =
by
return =
e-mail and delete this e-mail from your system. Unless =
explicitly
and =
conspicuously designated as "E-Contract Intended", this e-mail =
does
not =
constitute a contract offer, a contract amendment, or an =
acceptance
of a =
contract offer. This e-mail does not constitute a consent to =
the
use of =
sender's contact information for direct marketing purposes or =
for
transfers =
of data to third parties.
 
Francais =
Deutsch Italiano  Espanol  Portugues  Japanese  =
Chinese  Korean
 
       &nbs=
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------=_NextPart_000_000A_01C97F9A.5DBC6A50-- From owner-chemistry@ccl.net Mon Jan 26 09:45:01 2009 From: "=?utf-8?Q?St=C3=A9phane_T=C3=A9letch=C3=A9a?= steletch,+,free.fr" To: CCL Subject: CCL: Recommendations for computer hardware Message-Id: <-38508-090126065300-9113-NL5Gu+83N7neLvQKZtmFtg[A]server.ccl.net> X-Original-From: =?utf-8?Q?St=C3=A9phane_T=C3=A9letch=C3=A9a?= Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Date: Mon, 26 Jan 2009 12:13:15 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: =?utf-8?Q?St=C3=A9phane_T=C3=A9letch=C3=A9a?= [steletch_._free.fr] ----- "Rachelle Joyce Bienstock biensto1#niehs.nih.gov" a =C3=A9crit : > Sent to CCL by: "Rachelle Joyce Bienstock" [biensto1(-)niehs.nih.gov] >=20 >=20 > I am looking to purchase a new machine to run AMBER, CHARMm, > NAMD, Accelrys and Schrodinger software. I have already pretty much the same hw. > What would be your recommendations for a machine for optimum=20 > performance for these applications and this use (modeling, > visualization and simulation): >=20 > Processor: Intel Core Duo, 2 Duo, 2Quad, 2Extreme?? Take the most processors you can have on a chip, at least a quad since some= softwares (like Accelrys's)=20 are chip-based, and will run on 4 processors if they are on one chip but no= t on 2chip with 2 processors. > How many processors? Can the Schrodinger and > Accelrys software take advantage of and use multiple > processors of this kind? how many? are there particular processors > their software is optimized for? I cannot tell for Schrodinger but for Accelrys, then yes, you can use 4 pro= cessors (see above). > 32 bit or 64 bit Linux? =20 64 bits will allow you to benefit from the performance improvement is the s= oft is able to use it (for instance gromacs has a fair amount of performanc= e increase in double precision, 64bits mode). Moreover all 32bits applicati= ons run fine using 64bits linux install (you will only need to install some= 32bits libraries but they can install in parallel with 64 bits one so this= is not a problem). > How much memory is sufficient? A general rule would be aoubt 1 to 2 GB per processor (not core), so for a = 2core *4 processors, that would be 8GB to 16GB, depending on your choice. P= rovided memory is quite cheap, take as much as you need (but for running mo= lecular dynamics simulation 8GB is already sufficient). >=20 > What about stereo? Are there Linux Centos 5 drivers that support Open > GL stereo graphics with Nvidia Quadro FX cards? Take upstream nvidia drivers, you will be able to use all their capabilitie= s and acceleration natively. From owner-chemistry@ccl.net Mon Jan 26 10:20:00 2009 From: "Gerard Pujadas gerard.pujadas#gmail.com" To: CCL Subject: CCL: Looking for SDF files for known toxic molecules Message-Id: <-38509-090126095348-6872-jG+2aJsEGotFu9VG/hR7PA(a)server.ccl.net> X-Original-From: Gerard Pujadas Content-Type: multipart/alternative; boundary=0015174c1418ccdf88046163c942 Date: Mon, 26 Jan 2009 15:45:22 +0100 MIME-Version: 1.0 Sent to CCL by: Gerard Pujadas [gerard.pujadas]_[gmail.com] --0015174c1418ccdf88046163c942 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear CCL list subscribers, is there any SDF file of known toxic molecules available for training a program that predicts toxicity? with many thanks in advances yours sincerely Gerard --0015174c1418ccdf88046163c942 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear CCL list subscribers,

is there any SDF file of known toxic molecules available for training a program that predicts toxicity?

with many thanks in advances

yours sincerely

Gerard
--0015174c1418ccdf88046163c942-- From owner-chemistry@ccl.net Mon Jan 26 14:00:01 2009 From: "richard apodaca rich_apodaca]*[yahoo.com" To: CCL Subject: CCL: Looking for SDF files for known toxic molecules Message-Id: <-38510-090126133148-8006-V32kcj3TrDsV+xSGaFmT+A%%server.ccl.net> X-Original-From: richard apodaca Content-Type: text/plain; charset=us-ascii Date: Mon, 26 Jan 2009 09:31:34 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: richard apodaca [rich_apodaca^-^yahoo.com] Gerard, A few are listed here: http://cheminformatics.org/datasets/index.shtml#tox If you compile any new datasets of your own, how would you feel about attaching a license to it that allows free modification and redistribution? Putting the resulting file(s) under public revision control would be an interesting (and free) way of attracting collaborators around your work: http://depth-first.com/articles/2009/01/23/github-for-chemistry-revision-controlled-datasets Just a thought. Rich ___________________________________ Richard L. Apodaca http://depth-first.com Blog http://metamolecular.com Company --- On Mon, 1/26/09, Gerard Pujadas gerard.pujadas#gmail.com wrote: > From: Gerard Pujadas gerard.pujadas#gmail.com > Subject: CCL: Looking for SDF files for known toxic molecules > To: "Apodaca, Rich " > Date: Monday, January 26, 2009, 6:45 AM > Dear CCL list subscribers, > > is there any SDF file of known toxic molecules available > for training a > program that predicts toxicity? > > with many thanks in advances > > yours sincerely > > Gerard From owner-chemistry@ccl.net Mon Jan 26 18:33:00 2009 From: "Naser Eltaher Eltayeb nasertaha90]![yahoo.co.uk" To: CCL Subject: CCL:G: M O coefficients in ZINDO/S Message-Id: <-38511-090126183032-25914-sGpDLK6s7hQEu9gfCShCAg]~[server.ccl.net> X-Original-From: "Naser Eltaher Eltayeb" Date: Mon, 26 Jan 2009 18:30:28 -0500 Sent to CCL by: "Naser Eltaher Eltayeb" [nasertaha90[A]yahoo.co.uk] Dear All I am trying to get electronic absorption spectra for some compounds using ZINDO/S in G03. When I get the result file , I find some of Molecular orbital have negative coefficient and some have positive coefficients. At first I think just I have to consider the positive one, but when I check my orbital I find the HOMO-LUMO transition have negative value. My question is what is the meaning of the negative and positive coefficient? and which of them I have to consider to assign the absorption transitions. Excitation energies and oscillator strengths: Excited State 1: Singlet-A 2.8726 eV 431.61 nm f=0.2596 68 -> 71 0.35487 69 -> 70 0.58227 This state for optimization and/or second-order correction. Copying the excited state density for this state as the 1-particle RhoCI density. Excited State 2: Singlet-A 3.1979 eV 387.71 nm f=0.8095 67 -> 71 -0.10431 68 -> 70 0.44065 69 -> 71 0.50163 Excited State 3: Singlet-A 3.8469 eV 322.30 nm f=0.0602 63 -> 70 -0.15956 63 -> 71 0.12517 66 -> 73 0.10964 67 -> 70 0.13530 67 -> 71 -0.30128 68 -> 70 0.31133 68 -> 71 -0.11301 69 -> 71 -0.31036 69 -> 72 -0.21803 Thank you Naser Eltaher Eltayeb Universiti Sains Malaysia School of Chemical Sciences nasertaha90**yahoo.co.uk From owner-chemistry@ccl.net Mon Jan 26 19:35:00 2009 From: "N. Sukumar nagams!A!rpi.edu" To: CCL Subject: CCL:G: M O coefficients in ZINDO/S Message-Id: <-38512-090126193104-22416-DfGmdcsIzmVEJPGdxcv0kA++server.ccl.net> X-Original-From: "N. Sukumar" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Mon, 26 Jan 2009 19:30:48 -0500 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams .. rpi.edu] Electronic states are in general linear combinations of configuration state functions (excitations from the ground state in a CI treatment). Configurations with coefficients of the same sign interfere constructively with each other, configurations with coefficients of opposite sign interfere destructively with each other. The squares of the coefficients give the relative weights of the respective excitations in that excited state. Dr. N. Sukumar http://www.rpi.edu/research/biotech/researchers/sukumar.html ==============Original message text=============== On Mon, 26 Jan 2009 18:30:28 EST "Naser Eltaher Eltayeb nasertaha90]![yahoo.co.uk" wrote: Sent to CCL by: "Naser Eltaher Eltayeb" [nasertaha90[A]yahoo.co.uk] Dear All I am trying to get electronic absorption spectra for some compounds using ZINDO/S in G03. When I get the result file , I find some of Molecular orbital have negative coefficient and some have positive coefficients. At first I think just I have to consider the positive one, but when I check my orbital I find the HOMO-LUMO transition have negative value. My question is what is the meaning of the negative and positive coefficient? and which of them I have to consider to assign the absorption transitions. Excitation energies and oscillator strengths: Excited State 1: Singlet-A 2.8726 eV 431.61 nm f=0.2596 68 -> 71 0.35487 69 -> 70 0.58227 This state for optimization and/or second-order correction. Copying the excited state density for this state as the 1-particle RhoCI density. Excited State 2: Singlet-A 3.1979 eV 387.71 nm f=0.8095 67 -> 71 -0.10431 68 -> 70 0.44065 69 -> 71 0.50163 Excited State 3: Singlet-A 3.8469 eV 322.30 nm f=0.0602 63 -> 70 -0.15956 63 -> 71 0.12517 66 -> 73 0.10964 67 -> 70 0.13530 67 -> 71 -0.30128 68 -> 70 0.31133 68 -> 71 -0.11301 69 -> 71 -0.31036 69 -> 72 -0.21803 Thank you Naser Eltaher Eltayeb Universiti Sains Malaysia School of Chemical Sciences nasertaha90::yahoo.co.ukhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text=========== From owner-chemistry@ccl.net Mon Jan 26 22:20:01 2009 From: "Matthias Wirth wirth:-:bioinformatik.uni-frankfurt.de" To: CCL Subject: CCL: Looking for SDF files for known toxic molecules Message-Id: <-38513-090126143015-25903-GRN37/Jwo0g/DohHpkCG5g]-[server.ccl.net> X-Original-From: Matthias Wirth Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Mon, 26 Jan 2009 19:58:19 +0100 Mime-Version: 1.0 (Apple Message framework v930.3) Sent to CCL by: Matthias Wirth [wirth*o*bioinformatik.uni-frankfurt.de] Dear Gerard, There are the DSSTox datasets that might be useful for you. --> http://www.epa.gov/ncct/dsstox/DataFiles.html Cheers, Matthias On Jan 26, 2009, at 3:45 PM, Gerard Pujadas gerard.pujadas#gmail.com wrote: > Dear CCL list subscribers, > > is there any SDF file of known toxic molecules available for > training a program that predicts toxicity? > > with many thanks in advances > > yours sincerely > > Gerard From owner-chemistry@ccl.net Mon Jan 26 23:03:00 2009 From: "Kamalakar Jadhav kjadhav.!A!.vlifesciences.com" To: CCL Subject: CCL: Computational mutagenesis Message-Id: <-38514-090126230020-20106-0jtokRp/jbtQJvYadJjo0Q!A!server.ccl.net> X-Original-From: "Kamalakar Jadhav" Date: Mon, 26 Jan 2009 23:00:16 -0500 Sent to CCL by: "Kamalakar Jadhav" [kjadhav*vlifesciences.com] Hi Sebastian, VLifeMDS allows single amino acid mutations into protein structure with consideration of rotomers. It also provides facility of optimization. For more information www.vlifesciences.com From owner-chemistry@ccl.net Mon Jan 26 23:37:00 2009 From: "soumya samineni soumya_samineni_._rediffmail.com" To: CCL Subject: CCL: Nanowires and nanotubes Message-Id: <-38515-090126233150-8987-rcnfnP8Q9IyCn7cjmJ7ZKA * server.ccl.net> X-Original-From: "soumya samineni" Date: Mon, 26 Jan 2009 23:31:45 -0500 Sent to CCL by: "soumya samineni" [soumya_samineni,rediffmail.com] Dear CCL mates Can some one let me know how can i generate the coordinates of different nanotubes and nano wires of different materials eg. different types of Si nanotubes/nano wires. thanks in advance soumya