From owner-chemistry@ccl.net Thu Jun 28 01:25:01 2007 From: "Dr David N Haney haney**edusoft-lc.com" To: CCL Subject: CCL: looking for free software to generate descriptors Message-Id: <-34591-070627130505-18971-Y3QEVQEVoowf8wwUTYbDkQ!A!server.ccl.net> X-Original-From: Dr David N Haney Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 27 Jun 2007 12:17:45 -0400 Mime-Version: 1.0 Sent to CCL by: Dr David N Haney [haney!^!edusoft-lc.com] Dear Grace, There are probably some free descriptor generating software modules out there for Academia. EduSoft (http://www.edusoft-lc.com/molconn/) offers one of the most comprehensive softwares for the original Kier-Hall descriptors. This original program has been significantly updated and the number of descriptors expanded to several hundred. These descriptors are based on molecular connectivity and chemical graph theory. They are 1-D and 2-D values. There are not many programs that I am aware of that offer large 3-D descriptor sets. EduSoft also offers a simple "hydropathy" (evaluating hydrophobic and hydrophilic components) program, HintLogP (http://www.edusoft-lc.com/hint/) which will provide several 2-D and a few 3-D descriptors. Of course 3-D descriptors REQUIRE and absolute 3-D structure (not a guess from SMILES/Depict programs). These programs are not FREE, but we do offer an 80% discount to Academics. I believe that Mesa Analytics (http://www.mesaac.com/) may be developing some software for the classroom called "Virtual Classroom" that may be free for Academics. This software also includes the Molconn-Z descriptors. On Tue, Jun 26, 2007 at 04:22:34PM -0700, Grace Shen sll513_._yahoo.com wrote: > Dear All: > > Thank you all very much for the help regarding the "DOCK" question previously. Now I am wondering if anyone knows there is any free software which can help me to generate the regular common 1D, 2D and 3D descriptors so that I can perform QSAR analysis efficiently? Thanks, > > Cheers, > Grace Shen > > > > ____________________________________________________________________________________ > Need a vacation? Get great deals > to amazing places on Yahoo! Travel. > http://travel.yahoo.com/ -- ######### David N. Haney, Ph.D. ######### # EduSoft, LC Phone - 858-483-1197 # # 5455 Westknoll Dr. FAX - 858-483-1046 # # La Jolla, CA 92037 Email - haney[A]edusoft-lc.com # ################# ##################### From owner-chemistry@ccl.net Thu Jun 28 02:53:01 2007 From: "David A. Case case[]scripps.edu" To: CCL Subject: CCL: Lysine Acetylation Message-Id: <-34592-070627135631-27547-lAYADWMKX57yRq13EUle9A||server.ccl.net> X-Original-From: "David A. Case" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 27 Jun 2007 10:56:20 -0700 Mime-Version: 1.0 Sent to CCL by: "David A. Case" [case a scripps.edu] On Tue, Jun 26, 2007, Rodney E Versace herrklug_gott-x-yahoo.com wrote: > > Could anybody tell me how can I acetylate a lysine in the pdb, using amber9.0, please? You should direct amber-related questions to the Amber mailing list; see http://amber.scripps.edu for information on how to subscribe. Briefly, look at the "antechamber" section of the manual; there are some useful tutorials on preparing modified amino acids here: http://amber.scripps.edu/antechamber ...regards...dave case From owner-chemistry@ccl.net Thu Jun 28 04:05:01 2007 From: "Kim Hanjo lordmiss[a]gmail.com" To: CCL Subject: CCL: looking for free software to generate descriptors Message-Id: <-34593-070628031221-13690-mDOhVA78g9bRXxIRDFDMQw__server.ccl.net> X-Original-From: Kim Hanjo Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=EUC-KR Date: Thu, 28 Jun 2007 15:11:08 +0900 MIME-Version: 1.0 Sent to CCL by: Kim Hanjo [lordmiss : gmail.com] PreADMET is capable to calculate molecular descriptors and to predict ADME properties and toxicities. The desktop version is not free, but the web version is free with some restrictions (one molecule per one calculation, output is HTML). Visit to http://preadmet.bmdrc.org Grace Shen sll513_._yahoo.com wrote: > Dear All: > Thank you all very much for the help regarding the "DOCK" question > previously. Now I am wondering if anyone knows there is any free > software which can help me to generate the regular common 1D, 2D and > 3D descriptors so that I can perform QSAR analysis efficiently? Thanks, > /Cheers,/ > > /Grace Shen/ > > > ------------------------------------------------------------------------ > Never miss an email again! > Yahoo! Toolbar > > alerts you the instant new Mail arrives. Check it out. > From owner-chemistry@ccl.net Thu Jun 28 10:07:00 2007 From: "Sue L chsue2004{}yahoo.com" To: CCL Subject: CCL: Change in dipole moment from ground state to excited state Message-Id: <-34594-070628100356-5430-Kr20jGp+aWmT3wIi3h8WRQ ~~ server.ccl.net> X-Original-From: "Sue L" Date: Thu, 28 Jun 2007 10:03:53 -0400 Sent to CCL by: "Sue L" [chsue2004-x-yahoo.com] Hi Does anyone know how to calculate a change in dipole moment for transitions(ground state to excited state) in TDDFT calculation? Thank you very much! Sue From owner-chemistry@ccl.net Thu Jun 28 11:45:00 2007 From: "Marcel Swart marcel.swart _ icrea.es" To: CCL Subject: CCL: Change in dipole moment from ground state to excited state Message-Id: <-34595-070628113206-4495-oFUubBI8b8HYIDholY4Ciw * server.ccl.net> X-Original-From: Marcel Swart Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Date: Thu, 28 Jun 2007 17:31:10 +0200 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Marcel Swart [marcel.swart ~~ icrea.es] Dear Sue, what do you mean ? The difference in dipole moment between ground state and excited state, or the transition dipole moment ? Those are two different things, the latter should be given by standard TD-DFT, while for the former you need to do finite field calculations. How to obtain the dipole moment of the excited state can be found in the following paper: "Excited state polarizabilities of conjugated molecules calculated using time dependent density functional theory" F.C.Grozema, R.Telesca, H.T.Jonkman, L. Siebeles, J.G.Snijders J. Chem. Phys. 115, 2001, 10014-10021 On Jun 28, 2007, at 4:03 PM, Sue L chsue2004{}yahoo.com wrote: > > Sent to CCL by: "Sue L" [chsue2004-x-yahoo.com] > Hi > > Does anyone know how to calculate a change in dipole moment for > transitions(ground state to excited state) in TDDFT calculation? > > Thank you very much! > > Sue > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > =================================== dr. Marcel Swart ICREA researcher at Institut de Química Computacional Universitat de Girona Campus Montilivi 17071 Girona Catalunya (Spain) fax +34-972-418356 e-mail marcel.swart[#]icrea.es marcel.swart[#]udg.edu web http://www.icrea.es/pag.asp?id=Marcel.Swart http://iqc.udg.edu/~marcel =================================== From owner-chemistry@ccl.net Thu Jun 28 12:29:01 2007 From: "Aleksandra N Rudnitskaya Aleksandra.rudnit001 .. umb.edu" To: CCL Subject: CCL:G: opt of aluminum complexes Message-Id: <-34596-070628122601-27027-9I3vCGbzv2/m7ptwUsoXwg::server.ccl.net> X-Original-From: "Aleksandra N Rudnitskaya" Date: Thu, 28 Jun 2007 12:25:57 -0400 Sent to CCL by: "Aleksandra N Rudnitskaya" [Aleksandra.rudnit001=umb.edu] Dear CCL members, I have a problem with optimization of molecule that contains aluminum, oxygen, hydrogen, and silicon. The main problem is that I have a lot of doubly bridging oxygen sites. Those bridging bonds are different form regular bonds and aluminum, for example, has coordination number 6 instead of expected 3, or oxygen has coordination number 3 instead of usual 2. As fare as I can see, there are two problems, the first, how to draw the structure with bridging bonds correctly and, the second, using what basis set may I optimize this structure in Gaussian? Thank you very much in advance. Aleksandra From owner-chemistry@ccl.net Thu Jun 28 13:05:00 2007 From: "Agnieszka Urbanowicz agau#,#onet.eu" To: CCL Subject: CCL:G: Gaussian03 ECP Eu3+ Message-Id: <-34597-070628114904-7689-/skAWjy8bnoM1S8PLeKpsw%server.ccl.net> X-Original-From: "Agnieszka Urbanowicz" Date: Thu, 28 Jun 2007 11:49:00 -0400 Sent to CCL by: "Agnieszka Urbanowicz" [agau:-:onet.eu] I am a beginner in ECP techniques and I have trouble with define multiplicity of lanthanide complexes in Gaussian 03 input, for example ErCl3_6H2O? How can I calculate a multiplicity of this complex? Thank you in advance. Best Regards! /Aga U. agau-x-onet.eu From owner-chemistry@ccl.net Thu Jun 28 13:44:00 2007 From: "Lothar.Terfloth=chemie.uni-erlangen.de" To: CCL Subject: CCL: looking for free software to generate descriptors Message-Id: <-34598-070628084142-26006-zi4sDabLnpPKgaacSVbXbQ*server.ccl.net> X-Original-From: Lothar.Terfloth- -chemie.uni-erlangen.de Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 28 Jun 2007 13:45:39 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Lothar.Terfloth!A!chemie.uni-erlangen.de ADRIANA.Code available from Molecular Networks is able to calculate a series of molecular descriptors that can be applied in the area of in silico discovery and optimization of new chemical entities. The descriptors encode physicochemical, topological, geometrical and surface properties of molecules. More detailed information is available at the URL: http://www.mol-net.com/software/category/descriptors.html System Requirements: - Microsoft Windows NT/2000/XP - SUSE Linux (Release 8/9, Kernel 2.4/2.6 for x86, AMD64) - Red Hat Linux 8, 9, Enterprise (Kernel 2.4/2.6 for x86) - ADRIANA.Code is also available as component for Pipeline Pilot. A demo version is available on request after registration. With best regards, Lothar Terfloth -- -------------------------------------------------------- Dr. Lothar Terfloth Tel. +49-9131-9790623 Molecular Networks GmbH Fax: +49-9131-815 669 Henkestr. 91 D-91052 Erlangen Germany email: Lothar.Terfloth _ mol-net.com www: http://www.mol-net.com -------------------------------------------------------- > Dear All: > > Thank you all very much for the help regarding the "DOCK" question > previously. Now I am wondering if anyone knows there is any free software > which can help me to generate the regular common 1D, 2D and 3D descriptors > so that I can perform QSAR analysis efficiently? Thanks, > > Cheers, > Grace Shen > > > > ____________________________________________________________________________________ > Need a vacation? Get great deals > to amazing places on Yahoo! Travel. > http://travel.yahoo.com/ From owner-chemistry@ccl.net Thu Jun 28 14:14:00 2007 From: "Shobe, David David.Shobe^sud-chemie.com" To: CCL Subject: CCL:G: opt of aluminum complexes Message-Id: <-34599-070628140730-760-8UBvoV/Hs7aRqAksO07kdA===server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 28 Jun 2007 20:07:04 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe(a)sud-chemie.com] Aleksandra, Unless you're using a molecular mechanics method, the coordination numbers shouldn't matter. Perhaps the structure is tricky to draw, but it should be possible with a decent front-end. In particular there should be an option to increase the valence of the selected atom; e.g. this would change oxygen from divalent to trivalent. If that doesn't work, I suppose you can put in nitrogen for the oxygen and a transition metal for the aluminium. But you'd have to remember to change them manually later to the correct atoms. Your structure probably has a number of unusual (for the organic chemist) rings. Again, your Gaussian front-end program should have a means for adding a new bond between 2 selected elements. For a 4-membered ring, create the chain A-B-C-D, paying attention to things like dihedral angles, and then add a bond between A and D. You can use the "clean structure" option after that, but be prepared to go back to the "uncleaned" structure if you don't like the results! --David Shobe -----Original Message----- > From: owner-chemistry~!~ccl.net [mailto:owner-chemistry~!~ccl.net] Sent: Thursday, June 28, 2007 12:26 PM To: Shobe, David Subject: CCL:G: opt of aluminum complexes Sent to CCL by: "Aleksandra N Rudnitskaya" [Aleksandra.rudnit001=umb.edu] Dear CCL members, I have a problem with optimization of molecule that contains aluminum, oxygen, hydrogen, and silicon. The main problem is that I have a lot of doubly bridging oxygen sites. Those bridging bonds are different form regular bonds and aluminum, for example, has coordination number 6 instead of expected 3, or oxygen has coordination number 3 instead of usual 2. As fare as I can see, there are two problems, the first, how to draw the structure with bridging bonds correctly and, the second, using what basis set may I optimize this structure in Gaussian? Thank you very much in advance. Aleksandrahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Thu Jun 28 22:09:00 2007 From: "Sue Lam chsue2004===yahoo.com" To: CCL Subject: CCL: Change in dipole moment from ground state to excited state Message-Id: <-34600-070628164055-21615-mQgbazzxsHxkiqSAsLLzkw%a%server.ccl.net> X-Original-From: Sue Lam Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1301794278-1183059647=:90871" Date: Thu, 28 Jun 2007 12:40:47 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Sue Lam [chsue2004.:.yahoo.com] --0-1301794278-1183059647=:90871 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Marcel, Thank you for your information. I am looking the change in dipole moment from ground state to excited state. I would like to study the effect of the solvent on the energy of the transitions. Those should be related to the dipole moment for the ground and excited states. If an excited state has a larger dipole moment than a ground state, the transition energy to that excited state will be red shifted from the non-polar to polar solvent. "Marcel Swart marcel.swart _ icrea.es" wrote: Sent to CCL by: Marcel Swart [marcel.swart ~~ icrea.es] Dear Sue, what do you mean ? The difference in dipole moment between ground state and excited state, or the transition dipole moment ? Those are two different things, the latter should be given by standard TD-DFT, while for the former you need to do finite field calculations. How to obtain the dipole moment of the excited state can be found in the following paper: "Excited state polarizabilities of conjugated molecules calculated using time dependent density functional theory" F.C.Grozema, R.Telesca, H.T.Jonkman, L. Siebeles, J.G.Snijders J. Chem. Phys. 115, 2001, 10014-10021 On Jun 28, 2007, at 4:03 PM, Sue L chsue2004{}yahoo.com wrote: > > Sent to CCL by: "Sue L" [chsue2004-x-yahoo.com] > Hi > > Does anyone know how to calculate a change in dipole moment for > transitions(ground state to excited state) in TDDFT calculation? > > Thank you very much! > > Sue > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > =================================== dr. Marcel Swart ICREA researcher at Institut de Química Computacional Universitat de Girona Campus Montilivi 17071 Girona Catalunya (Spain) fax +34-972-418356 e-mail marcel.swart%a%icrea.es marcel.swart%a%udg.edu web http://www.icrea.es/pag.asp?id=Marcel.Swart http://iqc.udg.edu/~marcel ===================================http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- Be a better Globetrotter. Get better travel answers from someone who knows. Yahoo! Answers - Check it out. --0-1301794278-1183059647=:90871 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Dear Marcel,
 
Thank you for your information. I am looking the change in dipole moment from ground state to excited state. I would like to study the effect of the solvent on the energy of the transitions. Those should be related to the dipole moment for the ground and excited states. If an excited state has a larger dipole moment than a ground state, the transition energy to that excited state will be red shifted from the non-polar to polar solvent.

"Marcel Swart marcel.swart _ icrea.es" <owner-chemistry=-=ccl.net> wrote:

Sent to CCL by: Marcel Swart [marcel.swart ~~ icrea.es]
Dear Sue,

what do you mean ?
The difference in dipole moment between ground state and excited state,
or the transition dipole moment ?

Those are two different things, the latter should be given by
standard TD-DFT,
while for the former you need to do finite field calculations. How to
obtain the
dipole moment of the excited state can be found in the following paper:

"Excited state polarizabilities of conjugated molecules calculated
using time dependent density functional theory"
F.C.Grozema, R.Telesca, H.T.Jonkman, L. Siebeles, J.G.Snijders
J. Chem. Phys. 115, 2001, 10014-10021

On Jun 28, 2007, at 4:03 PM, Sue L chsue2004{}yahoo.com wrote:

>
> Sent to CCL by: "Sue L" [chsue2004-x-yahoo.com]
> Hi
>
> Does anyone know how to calculate a change in dipole moment for
> transitions(ground state to excited state) in TDDFT calculation?
>
> Thank you very much!
>
> Sue
>
>
>
> -= This is automatically added to each message by the mailing
> script =-
> To recover the email address of the author of the message, please
> change> Conferences: http://server.ccl.net/chemistry/announcements/
> conferences/
>
> Search Messages: http://www.ccl.net/htdig (login: ccl, Password:
> search)>
> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-
> +-+-+
>
>
>

===================================
dr. Marcel Swart

ICREA researcher at
Institut de Química Computacional
Universitat de Girona

Campus Montilivi
17071 Girona
Catalunya (Spain)

fax
+34-972-418356
e-mail
marcel.swart%a%icrea.es
marcel.swart%a%udg.edu
web
http://www.icrea.es/pag.asp?id=Marcel.Swart
http://iqc.udg.edu/~marcel
===================================


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