From owner-chemistry@ccl.net Thu Oct 5 06:16:01 2006 From: "Fco. Javier Modrego modrego . unizar.es" To: CCL Subject: CCL: ccl archive search Message-Id: <-32713-061005061236-1691-TLelH+xv4CTQ1FzsQAYAGQ[]server.ccl.net> X-Original-From: "Fco. Javier Modrego" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" Date: Thu, 5 Oct 2006 11:07:06 +0200 Mime-Version: 1.0 Sent to CCL by: "Fco. Javier Modrego" [modrego^unizar.es] Ehemm.. Well... It is even closer, just in front of you while you read this... read the automatic footer of the messages from the list... Cheer, F.J. Modrego >Sent to CCL by: Debasis Sengupta [dxs~!~cfdrc.com] > >Login : ccl >passwd: search >see the instruction in the login panel. > >Igor Filippov Contr igorf^helix.nih.gov wrote: > >>Sent to CCL by: "Igor Filippov [Contr]" [igorf~!~helix.nih.gov] >>I'm not sure, but I would try the obvious first:Cheers, >>Igor >> >>On Wed, 2006-10-04 at 14:40, Jozsef Csontos jozsefcsontos/acreighton.edu >>wrote: >>  >> >>>Sent to CCL by: Jozsef Csontos [jozsefcsontos++creighton.edu] >>>Dear Members, >>> >>>maybe I just missed something, but >>>how can I search in the ccl archive? >>>Where can I get username and password? >>> >>>Thanks, >>>Jozsef > >>    >>> > From owner-chemistry@ccl.net Thu Oct 5 09:06:00 2006 From: "CCDC Announce ccdc-announce#ccdc.cam.ac.uk" To: CCL Subject: CCL: Release of Gold v. 3.1 Message-Id: <-32714-061005052615-29656-+ybpW+XdPKBbkNKIEMN4BA#%#server.ccl.net> X-Original-From: "CCDC Announce" Date: Thu, 5 Oct 2006 05:26:15 -0400 Sent to CCL by: "CCDC Announce" [ccdc-announce^-^ccdc.cam.ac.uk] The Cambridge Crystallographic Data Centre are pleased to announce the release of GOLD version 3.1, software for ligand/protein docking. New Features included in v. 3.1: * Protein flexibility: GOLD can now be set up to allow a localised backbone movement or rotation of specified protein side chains. * Docking with localised soft VdW potentials: Useful for cases where small loop movements are known to occur * Scoring functions specific to heme-containing proteins * Scaffold match constraint: Tight atom-to-atom mapping of a scaffold substructure to a reference structure. * Override of rotatable bond assignment: User can control rotatable bond assignment for substructures that are not well treated by the default assignment protocols. For further information please visit http://www.ccdc.cam.ac.uk/life_sciences/gold/ For a 60 day evaluation copy, please contact admin() ccdc.cam.ac.uk From owner-chemistry@ccl.net Thu Oct 5 09:41:01 2006 From: "silviu p polosan Spol68:yahoo.com" To: CCL Subject: CCL:G: computer resources management Message-Id: <-32715-061004011829-18661-QB42uEgMSeBpRNGmPa3poQ],[server.ccl.net> X-Original-From: "silviu p polosan" Date: Wed, 4 Oct 2006 01:18:29 -0400 Sent to CCL by: "silviu p polosan" [Spol68%%yahoo.com] Hello all, Can someone tell me in detals how can I manage the resources of the computer for Gaussian calculations applied for large molecules (over 50 atoms)? I checked the sentence: %rwf=1,2000MB,.....,8,2000MB and MaxDisk=15000MB but I still have problems, even if in the Gaussian03W version D help, said there are no such problems. My system is P4, 2GHz, 512 MB and over 30GB free hardisk memory. Thank you From owner-chemistry@ccl.net Thu Oct 5 10:16:01 2006 From: "Colette FOULIE colette.foulie%x%wanadoo.fr" To: CCL Subject: CCL: electrostatic potential Message-Id: <-32716-061005050443-24983-lWH5YcGkJhbc1LcamlUB4A:server.ccl.net> X-Original-From: "Colette FOULIE" Date: Thu, 5 Oct 2006 05:04:42 -0400 Sent to CCL by: "Colette FOULIE" [colette.foulie..wanadoo.fr] Hi CCLers, I would like to calculate the electrostatic potential of proteins. Does anybody know a tool which represents the electrostatic potential of a molecule and a tool which calculates this potential starting from a pdb file for example? Thanks in advance, Colette FOULIE Laboratoire de Physique, Thorie de la Matire Condense CNRS UMR 5027, Universit de Bourgogne. 9 avenue Alain Savary B.P 47870, F-21078 Dijon Cedex, France Tel : 03.80.39.59.50 Fax: 03.80.39.59.61 colette.foulie:_:u-bourgogne.fr From owner-chemistry@ccl.net Thu Oct 5 10:51:01 2006 From: "montserrat barbany mbarbany*_*imim.es" To: CCL Subject: CCL: unsubscribe Message-Id: <-32717-061005100434-24033-zZs3tj0mi1sNC3eMdI79IQ-$-server.ccl.net> X-Original-From: "montserrat barbany" Date: Thu, 5 Oct 2006 10:04:33 -0400 Sent to CCL by: "montserrat barbany" [mbarbany~!~imim.es] Montserrat Barbany Puig mbarbany:+:imim.es From owner-chemistry@ccl.net Thu Oct 5 11:36:00 2006 From: "Adlane sayede adlane.sayede::gmail.com" To: CCL Subject: CCL: electrostatic potential Message-Id: <-32718-061005113506-7682-+Lrp0oyYXtwpPJYt7zBNTA_+_server.ccl.net> X-Original-From: "Adlane sayede" Content-Type: multipart/alternative; boundary="----=_Part_12500_19947076.1160062499932" Date: Thu, 5 Oct 2006 17:34:59 +0200 MIME-Version: 1.0 Sent to CCL by: "Adlane sayede" [adlane.sayede[]gmail.com] ------=_Part_12500_19947076.1160062499932 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi Colette , Vega zz can make the deal http://www.ddl.unimi.it/vega/download.htm Bonne fin de soir=E9e, Adlane On 10/5/06, Colette FOULIE colette.foulie%x%wanadoo.fr < owner-chemistry_+_ccl.net> wrote: > > Sent to CCL by: "Colette FOULIE" [colette.foulie..wanadoo.fr] > Hi CCLers, > I would like to calculate the electrostatic potential of proteins. > Does anybody know a tool which represents the electrostatic potential of = a > molecule and a tool which calculates this potential starting from a pdb f= ile > for example? > Thanks in advance, > Colette FOULIE > > Laboratoire de Physique, Thorie de la Matire Condense > CNRS UMR 5027, Universit de Bourgogne. > 9 avenue Alain Savary > B.P 47870, F-21078 Dijon Cedex, France > Tel : 03.80.39.59.50 > Fax: 03.80.39.59.61 > > colette.foulie[*]u-bourgogne.fr > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > > ------=_Part_12500_19947076.1160062499932 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi Colette ,

Vega zz can make the deal

http://www.ddl.unimi.it/vega/download.htm

Bonne fin de soir=E9e,

Adlane

On 10/5/06, Colette FOULIE colette.foulie%x%w= anadoo.fr <owner-chemistr= y_+_ccl.net> wrote:
Sent to CCL by: "Colette  FOULIE" [colette.foulie..wana= doo.fr]
Hi CCLers,
I would like to calculate the electrostatic potent= ial of proteins.
Does anybody know a tool which represents the electrost= atic potential of a molecule and a tool which calculates this potential sta= rting from a pdb file for example?
Thanks in advance,
Colette FOULIE

Laboratoire de Physique, Th= orie de la Matire Condense
CNRS UMR 5027, Universit de Bourgogne.
9 a= venue Alain Savary
B.P 47870, F-21078 Dijon Cedex, France
Tel : 03.80= .39.59.50
Fax: 03.80.39.59.61

colette.foulie[*]u-bourgogne.fr



-=3D This is automatically added to = each message by the mailing script =3D-
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------=_Part_12500_19947076.1160062499932-- From owner-chemistry@ccl.net Thu Oct 5 14:29:01 2006 From: "Nathaniel V. Nucci nvnucci===mail.med.upenn.edu" To: CCL Subject: CCL: electrostatic potential Message-Id: <-32719-061005130417-11468-EAB/jkHCwRf76aUv791/SA%server.ccl.net> X-Original-From: "Nathaniel V. Nucci" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 5 Oct 2006 12:04:04 -0400 MIME-Version: 1.0 Sent to CCL by: "Nathaniel V. Nucci" [nvnucci|-|mail.med.upenn.edu] This is easily done using Qnifft, developed and available free from Dr. Kim Sharp's group at University of Pennsylvania. See: http://crystal.med.upenn.edu/software.html to download the program. The results are readily visualized in PyMol. Cheers, Nathaniel -- Nathaniel V. Nucci Department of Biochemistry and Biophysics University of Pennsylvania Quoting "Colette FOULIE colette.foulie%x%wanadoo.fr" : > Sent to CCL by: "Colette FOULIE" [colette.foulie..wanadoo.fr] > Hi CCLers, > I would like to calculate the electrostatic potential of proteins. > Does anybody know a tool which represents the electrostatic potential of a > molecule and a tool which calculates this potential starting from a pdb file > for example? > Thanks in advance, > Colette FOULIE > > Laboratoire de Physique, Thorie de la Matire Condense > CNRS UMR 5027, Universit de Bourgogne. > 9 avenue Alain Savary > B.P 47870, F-21078 Dijon Cedex, France > Tel : 03.80.39.59.50 > Fax: 03.80.39.59.61 > > colette.foulie[*]u-bourgogne.fr> > > > From owner-chemistry@ccl.net Thu Oct 5 16:52:00 2006 From: "Alessandro Contini alessandro.contini a unimi.it" To: CCL Subject: CCL: electrostatic potential Message-Id: <-32720-061005120509-28475-fCiHbvz5e6DiYC1IRTpWYQ[#]server.ccl.net> X-Original-From: Alessandro Contini Content-transfer-encoding: 7BIT Content-type: text/plain Date: Thu, 05 Oct 2006 17:06:50 +0200 MIME-version: 1.0 Sent to CCL by: Alessandro Contini [alessandro.contini.:.unimi.it] Hi, the Swiss-PdbViewer should do the job http://www.expasy.org/spdbv/ you could also try APBS for more advanced calculations. http://apbs.sourceforge.net/ Obtained results can be displayed by VMD http://www.ks.uiuc.edu/Research/vmd/ Hope this help Alessandro Il giorno gio, 05/10/2006 alle 10.18 -0400, Colette FOULIE colette.foulie%x%wanadoo.fr ha scritto: > Sent to CCL by: "Colette FOULIE" [colette.foulie..wanadoo.fr] > Hi CCLers, > I would like to calculate the electrostatic potential of proteins. > Does anybody know a tool which represents the electrostatic potential of a molecule and a tool which calculates this potential starting from a pdb file for example? > Thanks in advance, > Colette FOULIE > > Laboratoire de Physique, Thorie de la Matire Condense > CNRS UMR 5027, Universit de Bourgogne. > 9 avenue Alain Savary > B.P 47870, F-21078 Dijon Cedex, France > Tel : 03.80.39.59.50 > Fax: 03.80.39.59.61 > > colette.foulie[*]u-bourgogne.fr> > > -- Dr. Alessandro Contini Istituto di Chimica Organica "Alessandro Marchesini" Universita' degli Studi di Milano, Facolta' di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini a unimi.it skype alessandrocontini From owner-chemistry@ccl.net Thu Oct 5 17:26:00 2006 From: "Miklos Vargyas mvargyas%%chemaxon.com" To: CCL Subject: CCL: electrostatic potential Message-Id: <-32721-061005125923-5548-pkzWBnxFKWBjKsteaQJt3w]_[server.ccl.net> X-Original-From: Miklos Vargyas Content-Type: multipart/alternative; boundary="------------080809050605010402010000" Date: Thu, 05 Oct 2006 18:10:16 +0200 MIME-Version: 1.0 Sent to CCL by: Miklos Vargyas [mvargyas.:.chemaxon.com] This is a multi-part message in MIME format. --------------080809050605010402010000 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi Colotte, you can use MarvinSpace by ChemAxon: http://www.chemaxon.com/marvinspace/ Beside the built in crude method for approximating EP, MarvinSpace supports Charmm grids, so you can use Charmm to calculate the potential and visualize the results in MarvinSpace. Here is an example picture: http://www.chemaxon.com/marvinspace/gallery/phi80.png Our software tools are free for academic users and non-commercial web sites. Follow this link if you would like to subscribe for the free usage or need more details: http://www.chemaxon.com/licensing.html Please note that you get full support with the academic license. You can try MarvinSpace online: http://www.chemaxon.com/marvinspace/#try. The MarvinSpace application is available in the Marvin Beans package that can be dowloaded at the Marvin site (locate the Download link at http://www.chemaxon.com/marvin/) . I hope you'll like it. Miklos Colette FOULIE colette.foulie%x%wanadoo.fr wrote: >Sent to CCL by: "Colette FOULIE" [colette.foulie..wanadoo.fr] >Hi CCLers, >I would like to calculate the electrostatic potential of proteins. >Does anybody know a tool which represents the electrostatic potential of a molecule and a tool which calculates this potential starting from a pdb file for example? >Thanks in advance, >Colette FOULIE > >Laboratoire de Physique, Thorie de la Matire Condense >CNRS UMR 5027, Universit de Bourgogne. >9 avenue Alain Savary >B.P 47870, F-21078 Dijon Cedex, France >Tel : 03.80.39.59.50 >Fax: 03.80.39.59.61 > >colette.foulie[*]u-bourgogne.fr> > > > > > --------------080809050605010402010000 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Colotte,

you can use MarvinSpace by ChemAxon: http://www.chemaxon.com/marvinspace/
Beside the built in crude method for approximating EP, MarvinSpace supports Charmm grids, so you can use Charmm to calculate the potential and visualize the results in MarvinSpace. Here is an example picture: http://www.chemaxon.com/marvinspace/gallery/phi80.png

Our software tools are free for academic users and non-commercial web sites. Follow this link if you would like to subscribe for the free usage or need more details: http://www.chemaxon.com/licensing.html
Please note that you get full support with the academic license.

You can try MarvinSpace online: http://www.chemaxon.com/marvinspace/#try.
The MarvinSpace application is available in the Marvin Beans package that can be dowloaded at the Marvin site (locate the Download link at http://www.chemaxon.com/marvin/).

I hope you'll like it.

Miklos


Colette FOULIE colette.foulie%x%wanadoo.fr wrote: 
Sent to CCL by: "Colette  FOULIE" [colette.foulie..wanadoo.fr]
Hi CCLers,
I would like to calculate the electrostatic potential of proteins.
Does anybody know a tool which represents the electrostatic potential of a molecule and a tool which calculates this potential starting from a pdb file for example?
Thanks in advance,
Colette FOULIE

Laboratoire de Physique, Thorie de la Matire Condense
CNRS UMR 5027, Universit de Bourgogne.
9 avenue Alain Savary
B.P 47870, F-21078 Dijon Cedex, France
Tel : 03.80.39.59.50
Fax: 03.80.39.59.61

colette.foulie[*]u-bourgogne.frE-mail to subscribers: CHEMISTRY[A]ccl.net or use:
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--------------080809050605010402010000-- From owner-chemistry@ccl.net Thu Oct 5 19:43:01 2006 From: "Jaime A Sanchez jasanc0*_*engr.uky.edu" To: CCL Subject: CCL: thermodynamic properties of materials from the density of states Message-Id: <-32722-061005165533-629-nZ2l7OzZ2qOPqmH5mvhRug===server.ccl.net> X-Original-From: "Jaime A Sanchez" Date: Thu, 5 Oct 2006 16:55:32 -0400 Sent to CCL by: "Jaime A Sanchez" [jasanc0:+:engr.uky.edu] Hello everyone, I was wondering if anyone had experience in calculating thermodynamic properties of materials from the density of states; I want to calculate the former from the Fourier transform of the velocity autocorrelation function, as obtained from molecular dynamics simulations. Thanks Jaime Sanchez