From owner-chemistry@ccl.net Thu Jan 17 06:31:01 2013 From: "Paulo J. Madeira pjamadeira(~)ff.ul.pt" To: CCL Subject: CCL: Avgadro does not read MOPAC2012 output file using the keyword PM7 Message-Id: <-48081-130117062439-11888-zReZYwU0ZOL7RNCARVBwLw/a\server.ccl.net> X-Original-From: "Paulo J. Madeira" Date: Thu, 17 Jan 2013 06:24:37 -0500 Sent to CCL by: "Paulo J. Madeira" [pjamadeira-,-ff.ul.pt] Hi Geoff Thanks for the tip. I will report the bug to Avogadro. After sending the message I installed an older version of Avogadro (V 1.0.1) and all works fine, it seems this happens with the new version of Avogadro when you perform a force calculation. Once again, thanks Paulo > "Geoffrey Hutchison geoffh(!)pitt.edu" wrote: > > Sent to CCL by: Geoffrey Hutchison [geoffh(_)pitt.edu] > > I'm trying the new PM7 hamiltonean in MOPAC2012 and Avogadro can't read the output file (Error message: Reading molecular file failed,...) when I > > While I do have a copy of MOPAC2012, I haven't run any PM7 calculations yet. As with anything else Avogadro-related, my suggestion is to report a bug, either to the bug-tracker or the mailing list: > > Avogadro bug tracker: http://sourceforge.net/p/avogadro/bugs/ > mailing list: avogadro-discuss.:.lists.sourceforge.net > > In this case, the bug tracker is probably the best, since you can easily upload an example file for us to examine. > > Thanks for reporting the bug! > -Geoff > > P.S. The Avogadro paper is finally out (and open access). Please cite this if you use Avogadro: > http://www.jcheminf.com/content/4/1/17 > > --- > Prof. Geoffrey Hutchison > Department of Chemistry > University of Pittsburgh > tel: (412) 648-0492 > email: geoffh.:.pitt.edu > web: http://hutchison.chem.pitt.edu/ > > From owner-chemistry@ccl.net Thu Jan 17 08:28:00 2013 From: "kamel kamel_mansouri*yahoo.fr" To: CCL Subject: CCL: E-Dragon error Message-Id: <-48082-130117043934-28895-wfqkPnprcf1AmWVsjtCkkA|*|server.ccl.net> X-Original-From: kamel Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 17 Jan 2013 10:39:27 +0100 MIME-Version: 1.0 Sent to CCL by: kamel [kamel_mansouri:_:yahoo.fr] Dear Edilson, Thank you for your interest in the Dragon software. You'll be contacted soon for more clarifications about the occured problem. Thanks and regards Kamel Le 16/01/2013 12:32, Edilson Beserra Filho edilsonbeserra{}gmail.com a écrit : > Sent to CCL by: "Edilson Beserra Filho" [edilsonbeserra * gmail.com] > > I'm calculating molecular parameters with the E-Dragon plataform. For some > analogues with para-nitro group the calculations presents error with values of > -999 for all descriptors. Only a few molecules presents this. What's happening? > The structures are in .sdf format and the program works well for many others > structures. > > Thanks for attention, > > Prof. Edilson Beserra> > > From owner-chemistry@ccl.net Thu Jan 17 09:10:00 2013 From: "Sergio Manzetti sergio.manzetti/a\gmx.com" To: CCL Subject: CCL: Database on crystals Message-Id: <-48083-130117090855-5648-l5oLo9itXFejfOI0sVxG8w*|*server.ccl.net> X-Original-From: "Sergio Manzetti" Content-Type: multipart/alternative; boundary="========GMXBoundary248651358431725490404" Date: Thu, 17 Jan 2013 15:08:45 +0100 MIME-Version: 1.0 Sent to CCL by: "Sergio Manzetti" [sergio.manzetti{}gmx.com] --========GMXBoundary248651358431725490404 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 8bit Dear CCLrs, is there a database of both modelled and crystallized geometries of various materials, which is free and open for all? Best wishes Sergio --========GMXBoundary248651358431725490404 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: quoted-printable Dear CCL= rs, is there a database of both modelled and crystallized geometries of var= ious materials, which is free and  open for all?
=20
=20 Best wishes
=20
=20 Sergio --========GMXBoundary248651358431725490404-- From owner-chemistry@ccl.net Thu Jan 17 10:23:00 2013 From: "Sergio Manzetti sergio.manzetti__gmx.com" To: CCL Subject: CCL:G: Basis sets and modelling approaches for metal clusters Message-Id: <-48084-130117101553-16012-EL6v3JN5Cc5oC4bTGHTVmg(a)server.ccl.net> X-Original-From: "Sergio Manzetti" Content-Type: multipart/alternative; boundary="========GMXBoundary13141358435744162638" Date: Thu, 17 Jan 2013 16:15:43 +0100 MIME-Version: 1.0 Sent to CCL by: "Sergio Manzetti" [sergio.manzetti\a/gmx.com] --========GMXBoundary13141358435744162638 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 8bit Dear all, which approach would you recommend if one wants to make a model for DFT calculations of a metal cluster Mn (n<10)? Are there basis sets that are more appropriate than others which are compatible with Gaussian, and which modelling approach would you recommend for making a small cluster model? All the best, Sergio --========GMXBoundary13141358435744162638 Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: quoted-printable Dear all= , which approach would you recommend if one wants to make a model for DFT c= alculations of a metal cluster Mn (n<10)? Are there basis sets that are = more appropriate than others which are compatible with Gaussian, and which = modelling approach would you recommend for making a small cluster model?=20
=20 All the  best,
=20
=20 Sergio --========GMXBoundary13141358435744162638-- From owner-chemistry@ccl.net Thu Jan 17 10:58:00 2013 From: "Geoffrey Hutchison geoffh#pitt.edu" To: CCL Subject: CCL: Database on crystals Message-Id: <-48085-130117102620-20626-8u7wwAD5DAkaqMmeXtamnw%%server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=windows-1252 Date: Thu, 17 Jan 2013 10:26:14 -0500 MIME-version: 1.0 (Apple Message framework v1283) Sent to CCL by: Geoffrey Hutchison [geoffh-*-pitt.edu] > Dear CCLrs, is there a database of both modelled and crystallized geometries of various materials, which is free and open for all? The Crystallography Open Database is, as you say, free an open. I’m not sure whether it includes theoretical crystal structures. http://www.crystallography.net There’s also a complete (theory and experiment) database of zeolite structures: http://www.iza-structure.org/databases/ Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh ~~ pitt.edu web: http://hutchison.chem.pitt.edu/ From owner-chemistry@ccl.net Thu Jan 17 11:33:00 2013 From: "Visvaldas K. coyote_v2002,+,yahoo.com" To: CCL Subject: CCL: Database on crystals Message-Id: <-48086-130117100929-12656-jSz+oIRP2eBkfno6QfdLxA||server.ccl.net> X-Original-From: "Visvaldas K." Content-Type: multipart/alternative; boundary="-158940594-1042769660-1358435361=:87799" Date: Thu, 17 Jan 2013 07:09:21 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: "Visvaldas K." [coyote_v2002 ~ yahoo.com] ---158940594-1042769660-1358435361=:87799 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable You can try Crystallography Open Database=0Ahttp://www.crystallography.net/= .=0ANo models there, though.=0A=0ABest regards,=0A=0AVis=0A=0A=0A=0A=0A____= ____________________________=0A From: Sergio Manzetti sergio.manzetti/agmx.= com =0ATo: "Kairys, Visvaldas " =0ASent: Thursday, January 17, 2013 4:08 PM=0ASubject: CCL: D= atabase on crystals=0A =0A=0ADear CCLrs, is there a database of both modell= ed and crystallized geometries of various materials, which is free and=A0 o= pen for all?=0A=0ABest wishes=0A=0ASergio ---158940594-1042769660-1358435361=:87799 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
You can try Crystallo= graphy Open Database
http://www.crystallography.net/.
No models there= , though.

Best regards,

Vis


From:<= /span> Sergio Manzetti sergio.manzetti/agmx.com <owner-chemistry[]ccl= .net>
To: "Kairys, = Visvaldas " <coyote_v2002[]yahoo.com>
Sent: Thursday, January 17, 2013 4:08 PM
<= b>Subject: CCL: Database on c= rystals

=0A
Dear CCLrs, is there a database of = both modelled and crystallized geometries of various materials, which is fr= ee and  open for all?
=0A
=0ABest wishes
=0A
=0ASergio= =0A


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---158940594-1042769660-1358435361=:87799-- From owner-chemistry@ccl.net Thu Jan 17 12:08:00 2013 From: "Jacco van de Streek jacco.vandestreek,+,sund.ku.dk" To: CCL Subject: CCL: Database on crystals Message-Id: <-48087-130117104600-30707-sF/Z4oayBIqknzUNeK1vzg#,#server.ccl.net> X-Original-From: Jacco van de Streek Content-Language: en-GB Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 17 Jan 2013 15:45:48 +0000 MIME-Version: 1.0 Sent to CCL by: Jacco van de Streek [jacco.vandestreek===sund.ku.dk] > Dear CCLrs, is there a database of both modelled and crystallized geometries of various materials, which is free and open for all? This database contains experimental crystal structures of small molecules, for free: http://www.crystallography.net/ If you work for an academic institution, your institution probably has a subscription to the Cambridge Structural Database (CSD), which is much more complete (contains more structures) and is of higher quality (each structure is checked): http://www.ccdc.cam.ac.uk If you have it, you might just as well use it. The word "geometries" in your question suggests that you are looking for molecular crystal structures. In practice, the experimental crystal structures have been split over several databases depending on the chemical composition, there are different databases for small molecules, for metals, for inorganics and for proteins. Which one do you need? I am not aware of a repository of freely available energy-minimised crystal structures. If you need pairs of experimental crystal structures and the same structure energy-minimised, you can find that for about 225 molecular crystal structures in the supplementary material to this paper: http://scripts.iucr.org/cgi-bin/paper?S0108768110031873 The paper is Open Access, the energy-minimised crystal structures (with dispersion-corrected Density Functional Theory) are available for free in the Supplementary Material, and the experimental crystal structures are all Open Access (that is why we used them). What do you exactly mean by "modelled"? Predicted? Energy-minimised at QM level? Energy-minimised at MM level? Best wishes, -- Dr Jacco van de Streek Department of Pharmacy University of Copenhagen From owner-chemistry@ccl.net Thu Jan 17 12:43:00 2013 From: "James Kirkpatrick james.a.kirkpatrick|*|gmail.com" To: CCL Subject: CCL: Database on crystals Message-Id: <-48088-130117102934-22363-T5iaU+XMWzCRBs9tsLStDw%%server.ccl.net> X-Original-From: James Kirkpatrick Content-Type: multipart/alternative; boundary=f46d04088f7b0ec6bd04d37da9c3 Date: Thu, 17 Jan 2013 15:29:27 +0000 MIME-Version: 1.0 Sent to CCL by: James Kirkpatrick [james.a.kirkpatrick###gmail.com] --f46d04088f7b0ec6bd04d37da9c3 Content-Type: text/plain; charset=ISO-8859-1 The Cambridge Crystallographic database: http://www.ccdc.cam.ac.uk/products/csd/ James On Thu, Jan 17, 2013 at 2:08 PM, Sergio Manzetti sergio.manzetti/agmx.com < owner-chemistry%x%ccl.net> wrote: > Dear CCLrs, is there a database of both modelled and crystallized > geometries of various materials, which is free and open for all? > > Best wishes > > Sergio --f46d04088f7b0ec6bd04d37da9c3 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
The Cambridge Crystallographic database:
<= div style>
htt= p://www.ccdc.cam.ac.uk/products/csd/

James=


=

On Thu, Jan 17, 2013 at 2:08 PM, Sergio = Manzetti sergio.manzetti/agmx.com <o= wner-chemistry%x%ccl.net> wrote:
Dear CCLrs, is there a database of both modelled and= crystallized geometries of various materials, which is free and=A0 open fo= r all?
=20
=20 Best wishes
=20
=20 Sergio

--f46d04088f7b0ec6bd04d37da9c3-- From owner-chemistry@ccl.net Thu Jan 17 13:18:00 2013 From: "Fedor Goumans goumans*scm.com" To: CCL Subject: CCL: Database on crystals Message-Id: <-48089-130117105819-3724-p9s2dhnW2yWPK2g8Ztp2qA!^!server.ccl.net> X-Original-From: Fedor Goumans Content-Type: multipart/alternative; boundary="------------070509090808000108040009" Date: Thu, 17 Jan 2013 16:57:23 +0100 MIME-Version: 1.0 Sent to CCL by: Fedor Goumans [goumans-.-scm.com] This is a multi-part message in MIME format. --------------070509090808000108040009 Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit Dear Sergio, Perhaps this is of use: http://openmopac.net/PM7_accuracy/Periodic_table_solids.html An extensive list of solids calculated with PM7 in MOPAC2012, compared with experimental data. Best wishes, Fedor On 1/17/2013 3:08 PM, Sergio Manzetti sergio.manzetti/agmx.com wrote: > Dear CCLrs, is there a database of both modelled and crystallized > geometries of various materials, which is free and open for all? > > Best wishes > > Sergio -- Dr. T. P. M. Goumans Business Developer Scientific Computing & Modelling NV (SCM) Vrije Universiteit, FEW, Theoretical Chemistry De Boelelaan 1083 1081 HV Amsterdam, The Netherlands T +31 20 598 7625 F +31 20 598 7629 E-mail: goumans/a\scm.com http://www.scm.com --------------070509090808000108040009 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 8bit
Dear Sergio,

Perhaps this is of use:
http://openmopac.net/PM7_accuracy/Periodic_table_solids.html
An extensive list of solids calculated with PM7 in MOPAC2012, compared with experimental data.

Best wishes,
Fedor

On 1/17/2013 3:08 PM, Sergio Manzetti sergio.manzetti/agmx.com wrote:
Dear CCLrs, is there a database of both modelled and crystallized geometries of various materials, which is free and  open for all?

Best wishes

Sergio 


-- 
Dr. T. P. M. Goumans
Business Developer
Scientific Computing & Modelling NV (SCM)
Vrije Universiteit, FEW, Theoretical Chemistry
De Boelelaan 1083
1081 HV Amsterdam, The Netherlands
T +31 20 598 7625
F +31 20 598 7629
E-mail: goumans/a\scm.com
http://www.scm.com
--------------070509090808000108040009-- From owner-chemistry@ccl.net Thu Jan 17 13:53:01 2013 From: "Michela Taufer taufer-.-udel.edu" To: CCL Subject: CCL: Fen Zi, a open-source CUDA code for GPU-based MD simulations, is now available for download in Google Code Message-Id: <-48090-130117115233-15714-yGGP5e/bi0doIbpsrsHzoQ(_)server.ccl.net> X-Original-From: Michela Taufer Content-Type: multipart/alternative; boundary="Apple-Mail=_A4CDE3B4-3A8A-4710-A289-6B09FEE9028C" Date: Thu, 17 Jan 2013 11:52:23 -0500 Mime-Version: 1.0 (Apple Message framework v1283) Sent to CCL by: Michela Taufer [taufer ~ udel.edu] --Apple-Mail=_A4CDE3B4-3A8A-4710-A289-6B09FEE9028C Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=windows-1252 Fen Zi (yun dong de Fen Zi =3D Moving MOLECULES) is a CUDA code that = enables large-scale, GPU-based MD simulations. In Fen Zi, the complete = MD simulation is performed on GPUs.=20 The code of Fen Zi is now available in Google Code at = http://code.google.com/p/fen-zi/. Let us know if you are using Fen Zi or = you want to help extending the code. Any help or feedback is welcome! Fen Zi currently includes: - NVT and NVE ensembles (NPT coming soon) - Force field: CHARMM force field, Flexible Water Models - Lennard-Jones interactions: Switching or shifting - Long distance electrostatic interactions: Ewald summation method and = Reaction field - Solvent: Explicit or implicit model; TIP3; Flexible SPC/Fw water model - Exclusion lists for VDW and electrostatic interactions: NBXMod from 1 = to 5 - Restraint potentials to probe the free energetic evaluation of = processes - Shake/Rattle bond constraints for atom=96atom bonds involving at least = one hydrogen atom in the bonded pair For further information contact fenzi*gcl.cis.udel.edu _________________________________________________ Michela Taufer David and Beverly J.C. Mills Career Development Chair Computer and Information Sciences Biomedical Engineering University of Delaware Phone: (302) 831 0071=20 Fax: (302) 831 8458 E-Mail: taufer*acm.org URL: http://www.cis.udel.edu/~taufer GCLab: http://gcl.cis.udel.edu D*H: http://docking.cis.udel.edu __________________________________________________ --Apple-Mail=_A4CDE3B4-3A8A-4710-A289-6B09FEE9028C Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=windows-1252
Fen Zi (yun dong de Fen Zi =3D Moving MOLECULES) is a CUDA code = that enables large-scale, = GPU-based MD simulations. In Fen Zi, the complete 
The code of Fen Zi is = now available in Google Code at http://code.google.com/p/fen-zi/= . Let us know if you are using Fen Zi or you want to help extending = the code. Any help or feedback is welcome!

Fen Zi currently = includes:
- NVT and NVE ensembles (NPT coming = soon)
- Force field: CHARMM force field, Flexible = Water Models
- Lennard-Jones interactions: Switching or = shifting
- Long distance electrostatic interactions: = Ewald summation method and Reaction field
- Solvent: Explicit or implicit model; TIP3; Flexible SPC/Fw = water model
- Exclusion lists for VDW and electrostatic = interactions: NBXMod from 1 to 5
- Restraint potentials to probe the free energetic evaluation of = processes
- Shake/Rattle bond constraints for = atom=96atom bonds involving at least one hydrogen atom in the bonded = pair

For further information contact fenzi*gcl.cis.udel.edu




_________________________________________________

Michela = Taufer
David and Beverly J.C. Mills Career = Development Chair
Computer and = Information Sciences
Biomedical = Engineering
University of Delaware

Phone: (302) 831 = 0071 
Fax: (302) 831 8458
E-Mail: taufer*acm.org
URL: http://www.cis.udel.edu/~taufer
GCLab: http://gcl.cis.udel.edu
D*H: = http://docking.cis.udel.edu
__________________________________________________



= --Apple-Mail=_A4CDE3B4-3A8A-4710-A289-6B09FEE9028C-- From owner-chemistry@ccl.net Thu Jan 17 15:58:01 2013 From: "Andrey Kalinichev kalinich#,#subatech.in2p3.fr" To: CCL Subject: CCL: Database on crystals Message-Id: <-48091-130117142755-25046-IbHNnayGGD5WxZHRsL75lQ|-|server.ccl.net> X-Original-From: Andrey Kalinichev Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Thu, 17 Jan 2013 20:27:24 +0100 MIME-Version: 1.0 Sent to CCL by: Andrey Kalinichev [kalinich^_^subatech.in2p3.fr] Here is one useful database for minerals and inorganic crystals: http://database.iem.ac.ru/mincryst/ Andrey Le 17/01/2013 15:08, Sergio Manzetti sergio.manzetti/agmx.com a écrit : > Dear CCLrs, is there a database of both modelled and crystallized > geometries of various materials, which is free and open for all? > > Best wishes > > Sergio From owner-chemistry@ccl.net Thu Jan 17 23:34:01 2013 From: "Arindam Ganguly arindamganguly===gmail.com" To: CCL Subject: CCL: Database on crystals Message-Id: <-48092-130117165942-15805-4Tp7HZ5ilwgcBnFeeMA/3g(!)server.ccl.net> X-Original-From: Arindam Ganguly Content-Type: multipart/alternative; boundary=f46d04083e0d49946804d3831c30 Date: Thu, 17 Jan 2013 16:59:35 -0500 MIME-Version: 1.0 Sent to CCL by: Arindam Ganguly [arindamganguly(-)gmail.com] --f46d04083e0d49946804d3831c30 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi All, This may be of help as well, http://www.tothcanada.com/pdf/MTK-2.0electronicreprint.pdf Arindam On Thu, Jan 17, 2013 at 2:27 PM, Andrey Kalinichev kalinich#,# subatech.in2p3.fr wrote: > > Sent to CCL by: Andrey Kalinichev [kalinich^_^subatech.in2p3.fr] > Here is one useful database for minerals and inorganic crystals: > > http://database.iem.ac.ru/**mincryst/ > > Andrey > > > Le 17/01/2013 15:08, Sergio Manzetti sergio.manzetti/agmx.com a =E9crit : > > Dear CCLrs, is there a database of both modelled and crystallized >> geometries of various materials, which is free and open for all? >> >> Best wishes >> >> Sergio >> > > > > -=3D This is automatically added to each message by the mailing script = =3D-> http://www.ccl.net/cgi-bin/**ccl/send_ccl_message http://www.ccl.net/cgi-bin/**ccl/send_ccl_message chemistry/announcements/**conferences/ > > Search Messages: http://www.ccl.net/chemistry/**searchccl/index.shtml http://www.ccl.net/spammers.**txt > > RTFI: http://www.ccl.net/chemistry/**aboutccl/instructions/ > > > --=20 Arindam Ganguly, Ph.D. Scientist, USP Applied Compendial Research-Spectrometry Laboratory http://www.linkedin.com/in/arindamganguly --f46d04083e0d49946804d3831c30 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi All,


Arindam<= br>
On Thu, Jan 17, 2013 at 2:27 PM, Andrey Kali= nichev kalinich#,#subatech.in2p3.fr <owner-chemistry[]ccl.net> wrote:

Sent to CCL by: Andrey Kalinichev [kalinich^_^subatech.in2p3.fr]
Here is one useful database for minerals and inorganic crystals:

http://da= tabase.iem.ac.ru/mincryst/

Andrey


Le 17/01/2013 15:08, Sergio Manzetti sergio.manzetti/agmx.com a =E9crit :
Dear CCLrs, is there a database of both modelled and crystallized
geometries of various materials, which is free and open for all?

Best wishes

Sergio



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY[]ccl.net or use:
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--
=

Arindam Ganguly, Ph.D.
Scientist, USP
Applied Compendial Research-= Spectrometry Laboratory
http://www.linkedin.com/in/arindamganguly

--f46d04083e0d49946804d3831c30--