From owner-chemistry@ccl.net Wed Nov 11 01:51:00 2009 From: "Sharan sara180681_-_gmail.com" To: CCL Subject: CCL: Software Tool? Message-Id: <-40655-091111012147-8674-a7qgesNppDYIfVI6l9LpTA:-:server.ccl.net> X-Original-From: Sharan Content-Type: multipart/alternative; boundary=0016e64dbdf4d9413f0478116533 Date: Wed, 11 Nov 2009 10:37:05 +0530 MIME-Version: 1.0 Sent to CCL by: Sharan [sara180681 : gmail.com] --0016e64dbdf4d9413f0478116533 Content-Type: text/plain; charset=ISO-8859-1 Dear all Is there any software that can increase the delta G or E (free energy or enthalpy) in an isothermal system for a molecule and do molecular dynamics, classical or otherwise? Thanks in advance with regards SARAVANAN.I Jr. Scientist Chemoinformatics http://www.linkedin.com/in/saravananilangovan --0016e64dbdf4d9413f0478116533 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear all


Is there any softw= are that can increase the delta G or E (free energy or enthalpy) in an isot= hermal system for a molecule and do molecular dynamics, classical or otherw= ise?

Thanks in advance


wi= th regards
SARAVANAN.I
Jr. Scientist Chemoinformatics

http:/= /www.linkedin.com/in/saravananilangovan
--0016e64dbdf4d9413f0478116533-- From owner-chemistry@ccl.net Wed Nov 11 04:51:01 2009 From: "aa aa,+,chemaxon.hu" To: CCL Subject: CCL: remove salts from compounds Message-Id: <-40656-091111043216-16924-9HCU1e1MCR8M9R9kX4ZUTQ%%server.ccl.net> X-Original-From: aa Content-Type: multipart/alternative; boundary="------------000800090903070906070204" Date: Wed, 11 Nov 2009 09:36:06 +0100 MIME-Version: 1.0 Sent to CCL by: aa [aa++chemaxon.hu] This is a multi-part message in MIME format. --------------000800090903070906070204 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit HI amit, ChemAxon Standardizer will do this. It is not free but is free (as are all tools) for academic research. See this page for more info and how to download. This page for free academic package signup. Cheers Alex PS - heads up on improvements on Standardizer in JChem 5.3 (due out v soon), we are introducing checking/fixing/conversion notification capabilities for structure files. 5.3 will be MarvinSketch only but will be formally a part of Standardizer soon after. amit dong dongamit123a/gmail.com wrote: > Hi, > > Is there any free tool that can be used for removing ions/salts from a > large library of compounds? > > Thanks > AD --------------000800090903070906070204 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit HI amit,

ChemAxon Standardizer will do this. It is not free but is free (as are all tools) for academic research. See this page for more info and how to download. This page for free academic package signup.

Cheers
Alex

PS - heads up on improvements on Standardizer in JChem 5.3 (due out v soon), we are introducing checking/fixing/conversion notification capabilities for structure files. 5.3 will be MarvinSketch only but will be formally a part of Standardizer soon after.


amit dong dongamit123a/gmail.com wrote:
Hi,
 
Is there any free tool that can be used for removing ions/salts > from a large library of compounds?
 
Thanks
AD
--------------000800090903070906070204-- From owner-chemistry@ccl.net Wed Nov 11 05:26:01 2009 From: "Gerd Neudert gneudert(~)web.de" To: CCL Subject: CCL: remove salts from compounds Message-Id: <-40657-091111044602-18256-IvAJbr+Q0jbpCp5LDjYSvA-.-server.ccl.net> X-Original-From: "Gerd Neudert" Date: Wed, 11 Nov 2009 04:45:58 -0500 Sent to CCL by: "Gerd Neudert" [gneudert]^[web.de] You can use fconv ('fconv -rs' for your task) which is available after free registration here: https://pc1664.pharmazie.uni-marburg.de:433/index.php?topic=download Best, Gerd Neudert neudert**staff.uni-marburg.de >amit dong wrote: >Hi, > >Is there any free tool that can be used for removing ions/salts from a large >library of compounds? > >Thanks >AD From owner-chemistry@ccl.net Wed Nov 11 06:01:01 2009 From: "Carlos F. Lagos carlos^^^cbuc.cl" To: CCL Subject: CCL: remove salts from compounds Message-Id: <-40658-091110173344-971-g+bOJAsHUFZje39bJoPcpg() server.ccl.net> X-Original-From: "Carlos F. Lagos" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0075_01CA324A.EA873A60" Date: Thu, 10 Sep 2009 19:14:24 -0400 MIME-Version: 1.0 Sent to CCL by: "Carlos F. Lagos" [carlos[]cbuc.cl] This is a multi-part message in MIME format. ------=_NextPart_000_0075_01CA324A.EA873A60 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Use ChemAxon standarizer ( www.chemaxon.com) free for academics QF Carlos F. Lagos Centre for Bioinformatics CBUC, Faculty of Biological Sciences Medicinal Chemistry Laboratory MCL, Faculty of Chemistry P. Universidad Catolica de Chile Portugal 49, Zocalo I 8330025 Santiago-Chile Phone: +56 2 3541911 I http://www.cbuc.cl _____ De: owner-chemistry+carlos==cbuc.cl]-[ccl.net [mailto:owner-chemistry+carlos==cbuc.cl]-[ccl.net] En nombre de amit dong dongamit123a/gmail.com Enviado el: Martes, 10 de Noviembre de 2009 17:38 Para: Lagos, Carlos F Asunto: CCL: remove salts from compounds Hi, Is there any free tool that can be used for removing ions/salts from a large library of compounds? Thanks AD ------=_NextPart_000_0075_01CA324A.EA873A60 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Use ChemAxon = standarizer (www.chemaxon.com) free for academics

 =

QF = Carlos F. Lagos
Centre for Bioinformatics CBUC, Faculty of Biological = Sciences

Medicinal = Chemistry Laboratory MCL, Faculty of Chemistry
P. Universidad Catolica de Chile
Portugal 49, Zocalo I 8330025 Santiago-Chile
Phone: +56 2 3541911 I http://www.cbuc.cl

 

=

 

De: owner-chemistry+carlos=3D=3Dcbuc.cl]-[ccl.net [mailto:owner-chemistry+carlos=3D=3Dcbuc.cl]-[ccl.net] En nombre de amit dong dongamit123a/gmail.com
Enviado el: Martes, 10 de Noviembre de 2009 17:38
Para: Lagos, Carlos F =
Asunto: CCL: remove salts = > from compounds

 

Hi,

 

Is there any free tool that can be used for removing ions/salts = > from a large library of compounds?

 

Thanks

AD



__________ Information from ESET NOD32 Antivirus, version of = virus signature database 4593 (20091110) __________

The message = was checked by ESET NOD32 Antivirus.

http://www.eset.com
------=_NextPart_000_0075_01CA324A.EA873A60-- From owner-chemistry@ccl.net Wed Nov 11 07:45:00 2009 From: "Yang Mingjun jeffle07#163.com" To: CCL Subject: CCL: Simulation Methods Message-Id: <-40659-091111074122-12502-fBht3qFGN25AyEERTNH8gw++server.ccl.net> X-Original-From: "Yang Mingjun" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="gb2312" Date: Wed, 11 Nov 2009 20:41:11 +0800 Mime-Version: 1.0 Sent to CCL by: "Yang Mingjun" [jeffle07#163.com] Dear all, We are going to monitor how the ligand enters into the binding pocket of a protein. I am not sure whether there are some simulation methods suitable for this question. And so request your suggestions and recommendations? Many thanks. Jeffrey ---- Chinese Academy of Sciences, China. From owner-chemistry@ccl.net Wed Nov 11 10:12:00 2009 From: "Egon Willighagen egon.willighagen-*-gmail.com" To: CCL Subject: CCL: new platform for questions about open data, open source, and open standards in cheminformatics Message-Id: <-40660-091111100950-20114-wBzRzJXyANFlptQ3dmwg1g**server.ccl.net> X-Original-From: Egon Willighagen Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 11 Nov 2009 16:09:18 +0100 MIME-Version: 1.0 Sent to CCL by: Egon Willighagen [egon.willighagen|gmail.com] Dear CCL-community, The Blue Obelisk has today started a new forum for information about Open Data, Open Source, and Open Standard in cheminformatics: http://blueobelisk.stackexchange.com/ Like the other StackOverflow-like websites, it is a forum where people can ask questions and other users answer. Moreover, answers can be edited and tuned, much like a wiki. The aim is not to replace CCL or any other platform, but a mere attempt to provide information to the cheminformatics community. Information on the exchange is licensed CC0, and can be freely copied into other platforms, such as CCL itself. The scope is deliberately very broad, but oriented around questions that have to deal with Open Data, Open Source, and Open Standards. We hope it will serve the community well, and I am personally looking forward to seeing your questions answered soon! Kind regards, Egon Willighagen -- Post-doc ]![ Uppsala University Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers From owner-chemistry@ccl.net Wed Nov 11 10:50:01 2009 From: "Stephen Bowlus chezbowlus(!)comcast.net" To: CCL Subject: CCL: Simulation Methods Message-Id: <-40661-091111104535-4616-NZ4N15fAzz7dxx17EBNK2Q^-^server.ccl.net> X-Original-From: Stephen Bowlus Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Wed, 11 Nov 2009 07:12:45 -0800 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Stephen Bowlus [chezbowlus() comcast.net] The theoretical and computational biophysics group at UIUC (makers of NAMD and VMD) were active in research on steered or constrained MD. There was at one time a simulation of the (un?)docking of a ligand on the site (I think it was estrogen and estrogen receptor?) and there is now something else - a glycerol channel, or some such. This is probably the method of choice, or would be the first thing I would try. Steve Bowlus On Nov 11, 2009, at 4:41 AM, Yang Mingjun jeffle07#163.com wrote: > > Sent to CCL by: "Yang Mingjun" [jeffle07#163.com] > Dear all, > > We are going to monitor how the ligand enters into the binding > pocket of a protein. > I am not sure whether there are some simulation methods suitable for > this question. > And so request your suggestions and recommendations? > > Many thanks. > > Jeffrey > ---- > Chinese Academy of Sciences, China. > > > > -= 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/> > From owner-chemistry@ccl.net Wed Nov 11 14:30:00 2009 From: "David Eisenberg david.eisen(0)gmail.com" To: CCL Subject: CCL: Electrostatic potential surface from NBO Message-Id: <-40662-091111142912-29279-P8kL3WMZvVRsvCjv3vv8LA%x%server.ccl.net> X-Original-From: "David Eisenberg" Date: Wed, 11 Nov 2009 14:29:08 -0500 Sent to CCL by: "David Eisenberg" [david.eisen]![gmail.com] Dear CCL community, Is there a way of displaying an electrostatic potential surface of a molecule, based on a NBO charge distribution calculation? I have Chem3D and Molekel, and NBO 5.0. Thanks, David Eisenberg Jerusalem From owner-chemistry@ccl.net Wed Nov 11 16:39:01 2009 From: "Yves Wang yves.wang^duke.edu" To: CCL Subject: CCL: Electrostatic potential surface from NBO Message-Id: <-40663-091111163144-17586-lh9FDXCUFRGoU9H75lzgPA|server.ccl.net> X-Original-From: Yves Wang Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 11 Nov 2009 16:00:35 -0500 MIME-Version: 1.0 Sent to CCL by: Yves Wang [yves.wang*duke.edu] David Eisenberg david.eisen(0)gmail.com wrote: > Sent to CCL by: "David Eisenberg" [david.eisen]![gmail.com] > Dear CCL community, > > Is there a way of displaying an electrostatic potential surface of a molecule, > based on a NBO charge distribution calculation? > > I have Chem3D and Molekel, and NBO 5.0. > > Thanks, > David Eisenberg > Jerusalem> > > Hi David, It seems to me that NBO only gives you partial charges on atoms, i.e. the Natural Population Analysis. I believe there should be some software that can determine the potential surface based on partial charges. It should be irrelevant NBO. Best, -- Yi(Yves) Wang Department of Biochemistry Structural Biology & Biophysics Program Duke University BS: University of Science and Technology of China School of Life Sciences, National Laboratory for Physical Sciences at Microscale Tel: +1-919-236-3307 (Cell) +1-919-684-0235 (Lab 1) +1-919-660-1634 (Lab 2) Office: A20 LSRC / 5301 FFSC E-Mail: yves.wang^^^duke.edu Mail: Box 90317, Chemistry Department From owner-chemistry@ccl.net Wed Nov 11 19:37:01 2009 From: "Bahman Roostaei bahman.roostaei|a|utsa.edu" To: CCL Subject: CCL:G: Gaussian ZINDO ground state Message-Id: <-40664-091111193513-26101-l83xR0quMRdR1i/T7VXnyQ .. server.ccl.net> X-Original-From: "Bahman Roostaei" Date: Wed, 11 Nov 2009 19:35:09 -0500 Sent to CCL by: "Bahman Roostaei" [bahman.roostaei,,utsa.edu] Hi everybody, As a newly entered individual into this field, I am trying to clear out some concepts for myself. My confusion is in Gaussian Zindo. The Gaussian Zindo includes some sort of CI calculation. Why Gaussian does not report the CI coefficients for the first eigenstate of the CI Hamiltonian ? it always starts with reporting the CI coefficients of the first excited state. am I missing something here ? is it because the ground state of the Zindo-CI is the same as HF ground state ? If that's true why the SCF density is not diagonalized in the output? Thanks. Bahman. From owner-chemistry@ccl.net Wed Nov 11 23:25:00 2009 From: "Dalila Hammoutene dhammoutene^gmail.com" To: CCL Subject: CCL: Colloque PAMO-JSM 2010 Message-Id: <-40665-091111031940-10947-qohBWnZLWN1gX2CvNlL6Yw]_[server.ccl.net> X-Original-From: "Dalila Hammoutene" Date: Wed, 11 Nov 2009 03:19:37 -0500 Sent to CCL by: "Dalila Hammoutene" [dhammoutene[]gmail.com] Cher(e)s CCL(s), Veuillez trouver ci-joint la premiere circulaire pour le colloque PAMO-JSM 2010, qui se droulera a Orsay du 29 juin au 2 juillet 2010. Cette premiere circulaire concerne l'appel d'offres pour la mise en place de mini-colloques. Bien cordialement, Pour le comite d'organisation, Dr Olivier DULIEU Directeur de Recherches CNRS Laboratoire Aime Cotton, CNRS, bat. 505, Universite Paris-Sud XI, 91405 Orsay, Cedex, FRANCE. Tel: +33-169352013 Fax: +33-169410156 www.pamojsm2010.fr