From owner-chemistry@ccl.net Wed Sep 5 00:43:01 2007 From: "chupvl chupvl%%gmail.com" To: CCL Subject: CCL: Protein Flexibility Analysis Message-Id: <-35083-070904115532-11218-CmF2jIwuX2bb64/HLKUT0Q^^server.ccl.net> X-Original-From: chupvl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 04 Sep 2007 18:58:15 +0400 MIME-Version: 1.0 Sent to CCL by: chupvl [chupvl**gmail.com] Hello, you can make it with any molecular dynamics or NMA software http://en.wikipedia.org/wiki/Molecular_dynamics NMA software example http://www.igs.cnrs-mrs.fr/elnemo/ Chupakhin Vladimir, Dpt. of Chemistry, Moscow State University, Moscow, Russia Konrad Hinsen hinsen-.-cnrs-orleans.fr wrote: > Sent to CCL by: "Konrad Hinsen" [hinsen##cnrs-orleans.fr] > >> Sent to CCL by: "Sina T reli" [sinatureli]|[gmail.com] >> Hello, >> >> Do you know any software that can make protein flexibility analysis >> other than M^2AP and FIRST, which I am already aware of. >> > > Please have a look at DomainFinder, available from > > http://dirac.cnrs-orleans.fr/DomainFinder/ > > - > --------------------------------------------------------------------- > Konrad Hinsen > Centre de Biophysique Molculaire, CNRS Orlans > Synchrotron Soleil - Division Expriences > Saint Aubin - BP 48 > 91192 Gif sur Yvette Cedex, France > Tel. +33-1 69 35 97 15 > E-Mail: hinsen%%cnrs-orleans.fr > ---------------------------------------------------------------------> > > > > From owner-chemistry@ccl.net Wed Sep 5 01:43:01 2007 From: "Dr. Ponnadurai Ramasami ramchemi _ intnet.mu" To: CCL Subject: CCL:G: error in using the B3LYP/aug-cc-TZVP Message-Id: <-35084-070904225454-4793-7pB8CCeJes4V+1jLUcwD0w.@.server.ccl.net> X-Original-From: "Dr. Ponnadurai Ramasami" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Wed, 5 Sep 2007 05:54:41 +0400 MIME-Version: 1.0 Sent to CCL by: "Dr. Ponnadurai Ramasami" [ramchemi..intnet.mu] it should be B3LYP/aug-cc-TZVP opt freq no comma between opt and freq you can also add options to these keywords like opt=tight freq=raman ramasami ----- Original Message ----- > From: "Lalitha selvam lalithasel#%#rediffmail.com" To: "Ramasami, Ponnadurai " Sent: Wednesday, September 05, 2007 4:12 AM Subject: CCL:G: error in using the B3LYP/aug-cc-TZVP > > Sent to CCL by: "Lalitha selvam" [lalithasel(a)rediffmail.com] > Hello all.. > > I want to use B3LYP/aug-cc-TZVP with gaussian 03 for the optimised > structure with B3LYP/6-311G**. > but when I am running the input file, its giving me error like this: > > > "QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE. > B3LYP/aug-cc-TZVP opt,freq > ' > Last state="GCL" > TCursr= 909 LCursr= 7 > Error termination via Lnk1e in /usr/people/g03/l1.exe > > How to rectify and wats the problem in using this basis set.. > > Regards > Lalitha> > From owner-chemistry@ccl.net Wed Sep 5 03:16:00 2007 From: "Tanguy Van Regemorter tanguy.vr() yucom.be" To: CCL Subject: CCL:G: can i use MPW1K method in Gaussian 03 Message-Id: <-35085-070904112243-25712-8ioe+jfcGJnTQQtXcplU3w*o*server.ccl.net> X-Original-From: "Tanguy Van Regemorter" Date: Tue, 4 Sep 2007 11:22:39 -0400 Sent to CCL by: "Tanguy Van Regemorter" [tanguy.vr^^yucom.be] Hello Nagesh, Sometimes, when the functional is recent, you can not use the name of the functional as keyword. After checking on internet, it seems that you need to put this keyword: mpwpw91/6-31+G(d,p) IOp(3/76=0572004280) in order to be able to run the MPW1K. Here is the web page from where I took this information: http://comp.chem.umn.edu/info/DFT.htmmpw1k Otherwise, interesting information might be available on the original paper presenting the functional. Good luck ! Regards, Tanguy Van Regemorter ---------- Initial header ----------- > From : owner-chemistry{=}ccl.net To : "Van Regemorter, Tanguy -id3si-" tanguy.vr{=}yucom.be CC : Date : Mon, 3 Sep 2007 13:31:56 -0400 Subject : CCL:G: can i use MPW1K method in Gaussian 03 > > Sent to CCL by: "nagesh idupulapati" [nbi002[*]latech.edu] > > hello everyone > > I want to use MPW1K method for obtaining saddle-point geometries with gaussian 03. > > but when Iam typing the keyword in the input file, its giving me error like this: > > > "QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE. > MPW1K/6-31++G(D,P) OPT=(TS,NOEIGENTEST > ' > Last state="GCL" > TCursr= 1020 LCursr= 2 > Error termination via Lnk1e in /usr/people/g03/l1.exe at Mon Sep 3 12:56:11 2007." > > > Can anybody help me with this problem? > > Regards > > Nagesh From owner-chemistry@ccl.net Wed Sep 5 12:54:00 2007 From: "Alex A. Granovsky gran++classic.chem.msu.su" To: CCL Subject: CCL: The final PC GAMESS v. 7.1 release announcement Message-Id: <-35086-070905124241-29083-8A7PWutEn+Q9E29Nn4SLQw-.-server.ccl.net> X-Original-From: "Alex A. Granovsky" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="koi8-r" Date: Wed, 5 Sep 2007 20:59:39 +0400 MIME-Version: 1.0 Sent to CCL by: "Alex A. Granovsky" [gran(_)classic.chem.msu.su] Dear GAMESS users, I am proud to inform you that the final, official version of the PC GAMESS v. 7.1 was released today and is available from the PC GAMESS download site at ISU: http://www.msg.chem.iastate.edu/GAMESS/pcgamess.html The PC GAMESS page at MSU was updated as well: http://classic.chem.msu.su/gran/gamess/ Our big thanks to all testers of the intermediate PC GAMESS releases! As compared with the previous public release v. 7.0.1, PC GAMESS v. 7.1 includes the following enhancements and new features: newly developed very efficient serial and parallel MP2 gradient program, state-specific gradients for state-averaged MCSCF, much faster multithreaded MCQDPT code for large-scale jobs, faster, more robust PCM code with parallel mode support, improved Linux compatibility, NPTL-based dynamically linked binaries, initial optimization for Intel Penryn/Harpertown and AMD Barcelona processors, and many other improvements and performance enhancements. We are strongly encouraging all PC GAMESS users to upgrade to the most recent binaries. Beta testers, please upgrade as well, as there are several known bugs in the intermediate releases. Best regards, Alex Granovsky ------------------------- Dr. Alex A. Granovsky The PC GAMESS project, Laboratory of Chemical Cybernetics, Moscow State University From owner-chemistry@ccl.net Wed Sep 5 14:20:01 2007 From: "George Fitzgerald gxf=-=accelrys.com" To: CCL Subject: CCL:G: Materials Studio 4.2 available now from Accelrys Message-Id: <-35087-070905140433-24504-jrCl9C53LzcYN7C5MMvWgg]*[server.ccl.net> X-Original-From: "George Fitzgerald" Date: Wed, 5 Sep 2007 14:04:30 -0400 Sent to CCL by: "George Fitzgerald" [gxf(-)accelrys.com] Dear Computational Chemists Accelrys announces the availability of Materials Studio 4.2. New modules include o Gaussian(r) UI - a graphical interface to Gaussian 03 o Adsorption Locator - a simulated annealing tool for docking guest molecules to surfaces or onto nanoclusters Other new features include o New modules accessible through the MaterialsScript API: DMol3, Polymorph, Reflex Powder Refinement, Reflex Powder Crystallinity, and Reflex QPA o New Reflex tool for predicting the degree of crystallinity of a sample o Graphical builder for mesoscale templates o Force field fitting tools for GULP o Additional analysis capabilities in Forcite. For more information please visit the Materials Studio 4.2 web site at http://www.accelrys.com/products/mstudio/materials_studio_42.html All the best, George Fitzgerald From owner-chemistry@ccl.net Wed Sep 5 14:54:00 2007 From: "=?ISO-8859-1?Q?Sina_T=FCreli?= sinatureli]^[gmail.com" To: CCL Subject: CCL: Protein Flexibility Analysis Message-Id: <-35088-070905142550-28120-dQzLCgldDzoBooaMiet3ug : server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?Sina_T=FCreli?=" Content-Type: multipart/alternative; boundary="----=_Part_11708_26069048.1189013277442" Date: Wed, 5 Sep 2007 20:27:57 +0300 MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?Sina_T=FCreli?=" [sinatureli**gmail.com] ------=_Part_11708_26069048.1189013277442 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello, I have used spartan and hyperchem quite alot. I didnt know molecular dynamics software such as namd could be used to find the flexible residues in proteins. I will look into this topic more. Thanks. On 9/4/07, chupvl chupvl%%gmail.com wrote: > > > Sent to CCL by: chupvl [chupvl**gmail.com] > > Hello, > > you can make it with any molecular dynamics or NMA software > http://en.wikipedia.org/wiki/Molecular_dynamics > NMA software example http://www.igs.cnrs-mrs.fr/elnemo/ > > Chupakhin Vladimir, > Dpt. of Chemistry, Moscow State University, > Moscow, Russia > > Konrad Hinsen hinsen-.- cnrs-orleans.fr wrote: > > Sent to CCL by: "Konrad Hinsen" [hinsen##cnrs-orleans.fr] > > > >> Sent to CCL by: "Sina T reli" [sinatureli]|[ gmail.com] > >> Hello, > >> > >> Do you know any software that can make protein flexibility analysis > >> other than M^2AP and FIRST, which I am already aware of. > >> > > > > Please have a look at DomainFinder, available from > > > > http://dirac.cnrs-orleans.fr/DomainFinder/ > > > > - > > --------------------------------------------------------------------- > > Konrad Hinsen > > Centre de Biophysique Molculaire, CNRS Orlans > > Synchrotron Soleil - Division Expriences > > Saint Aubin - BP 48 > > 91192 Gif sur Yvette Cedex, France > > Tel. +33-1 69 35 97 15 > > E-Mail: hinsen%%cnrs-orleans.fr > > ---------------------------------------------------------------------> > > > ------=_Part_11708_26069048.1189013277442 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello,

I have used spartan and hyperchem quite alot. I didnt know molecular dynamics software such as namd could be used to find the flexible residues in proteins. I will look into this topic more. Thanks.

On 9/4/07, chupvl chupvl%%gmail.com <owner-chemistry:_:ccl.net> wrote:

Sent to CCL by: chupvl [chupvl**gmail.com]

Hello,

you can make it with any molecular dynamics or NMA software
http://en.wikipedia.org/wiki/Molecular_dynamics
NMA software example http://www.igs.cnrs-mrs.fr/elnemo/

Chupakhin Vladimir,
Dpt. of Chemistry, Moscow State University,
Moscow, Russia

Konrad Hinsen hinsen-.- cnrs-orleans.fr wrote:
> Sent to CCL by: "Konrad  Hinsen" [hinsen##cnrs- orleans.fr]
>
>> Sent to CCL by: "Sina  T  reli" [sinatureli]|[ gmail.com]
>> Hello,
>>
>> Do you know any software that can make protein flexibility analysis
>> other than M^2AP and FIRST, which I am already aware of.
>>
>
> Please have a look at DomainFinder, available from
>
>     http://dirac.cnrs-orleans.fr/DomainFinder/
>
> -
> ---------------------------------------------------------------------
> Konrad Hinsen
> Centre de Biophysique Molculaire, CNRS Orlans
> Synchrotron Soleil - Division Expriences
> Saint Aubin - BP 48
> 91192 Gif sur Yvette Cedex, France
> Tel. +33-1 69 35 97 15
> E-Mail: hinsen%%cnrs-orleans.fr
> --------------------------------------------------------------------->
>
>
>
>



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------=_Part_11708_26069048.1189013277442-- From owner-chemistry@ccl.net Wed Sep 5 22:22:01 2007 From: "immanuel feng feng.immanuel]=[gmail.com" To: CCL Subject: CCL: Computational Chemistry and Molecular Imaging Message-Id: <-35089-070905221841-16878-7EA6BptAazYmb+2Y0GGhaA!A!server.ccl.net> X-Original-From: "immanuel feng" Content-Type: multipart/alternative; boundary="----=_Part_19256_2688911.1189045111458" Date: Thu, 6 Sep 2007 10:18:31 +0800 MIME-Version: 1.0 Sent to CCL by: "immanuel feng" [feng.immanuel()gmail.com] ------=_Part_19256_2688911.1189045111458 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi, I am doing the physical organic chemistry calculations. I am curious about Molecular imaging and want to learn more, could I join your discussion group? 2007/8/31, Gustavo A Mercier gustavo.mercier+/-bmc.org < owner-chemistry-#-ccl.net>: > > > Sent to CCL by: "Gustavo A Mercier" [gustavo.mercier===bmc.org] > Hi! > > I am interested in the application of computatinal chemistry in the > development of molecular imaging agents, and contrast media in general. In > the past I did work on a putative MRI contrast agent based on a Manganese > Metalloporphyrin. > > With the recent introduction of a new journal, 'Contrast Media', database, > MICAD, and interest group by the Society of Nuclear Medicine (Molecular > Imaging), the time seems right to identify those members of the > computational chemistry community whose interest is in the development of > molecular imaging agents and contrast media. > > My interest is to exchange ideas, and see how we could promote > computational chemistry as a means to expedite the development of new > molcular imaging agents and contrast media. > > It seems to me that even within the chemistry community, this endeavor > remains a small fraction of the work done by computational chemists. It also > seems relatively unknown among the larger radiology/nuclear medicine > departments that work on developing such agents. > > I am sending this e-mail to the CCL community in the hopes of compiling a > list of individuals with interest in this field. If you would like to start > a special interest group (for now simple exchange of e-mail addresses), > please let me know. > > Thank you for your time! > > -- > Gustavo A. Mercier, Jr. MD,PhD > Boston Medical Center > Radiology - Nuclear Medicine > gamercier===yahoo.com (preferred e-mail address) > Gustavo.Mercier===bmc.org > gumercie===bu.edu> > > > ------=_Part_19256_2688911.1189045111458 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi, I am doing the physical organic chemistry calculations. I am curious about Molecular imaging and want to learn more, could I join your discussion group?

2007/8/31, Gustavo A Mercier gustavo.mercier+/-bmc.org <owner-chemistry-#-ccl.net>:

Sent to CCL by: "Gustavo A Mercier" [gustavo.mercier===bmc.org]
Hi!

I am interested in the application of computatinal chemistry in the development of molecular imaging agents, and contrast media in general. In the past I did work on a putative MRI contrast agent based on a Manganese Metalloporphyrin.

With the recent introduction of a new journal, 'Contrast Media', database, MICAD, and interest group by the Society of Nuclear Medicine (Molecular Imaging), the time seems right to identify those members of the computational chemistry community whose interest is in the development of molecular imaging agents and contrast media.

My interest is to exchange ideas, and see how we could promote computational chemistry as a means to expedite the development of new molcular imaging agents and contrast media.

It seems to me that even within the chemistry community, this endeavor remains a small fraction of the work done by computational chemists. It also seems relatively unknown among the larger radiology/nuclear medicine departments that work on developing such agents.

I am sending this e-mail to the CCL community in the hopes of compiling a list of individuals with interest in this field. If you would like to start a special interest group (for now simple exchange of e-mail addresses), please let me know.

Thank you for your time!

--
Gustavo A. Mercier, Jr. MD,PhD
Boston Medical Center
Radiology - Nuclear Medicine
gamercier===yahoo.com (preferred e-mail address)
Gustavo.Mercier===bmc.org
gumercie===bu.edu



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