From owner-chemistry@ccl.net Tue Dec 18 03:53:00 2012 From: "Sobia A Halim sobia_halim]~[yahoo.com" To: CCL Subject: CCL: protein ligand complex simulation on NAMD Message-Id: <-48003-121218035132-30189-YpXHWVMRq+F54Ur+Cz4CTA[-]server.ccl.net> X-Original-From: "Sobia A Halim" Date: Tue, 18 Dec 2012 03:51:31 -0500 Sent to CCL by: "Sobia A Halim" [sobia_halim|a|yahoo.com] Dear All I am using NAMD for protein-ligand-membrane complex simulation. Please anyone let me know how to generate ligand parameters and topology file. With best wishes and thanks in advance Sobia From owner-chemistry@ccl.net Tue Dec 18 04:43:00 2012 From: "=?ISO-8859-1?Q?R=F3bert_Kiss?= rkiss^mcule.com" To: CCL Subject: CCL: 1-Click Docking Message-Id: <-48004-121218043201-14370-7zAIA6Kqskj/51v0J6jqrQ_._server.ccl.net> X-Original-From: =?ISO-8859-1?Q?R=F3bert_Kiss?= Content-Type: multipart/alternative; boundary=e89a8f234ab1317c8404d11d2b02 Date: Tue, 18 Dec 2012 10:31:55 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?R=F3bert_Kiss?= [rkiss _ mcule.com] --e89a8f234ab1317c8404d11d2b02 Content-Type: text/plain; charset=ISO-8859-1 Molecular docking has never been easier! Mcule.com , the online drug discovery platform, is pleased to announce the release of the easiest molecular docking solution online: 1-Click Docking . Draw a ligand, select a target, click on Dock and start browsing the results! Try 1-Click Docking now! It is FREE: https://mcule.com/apps/1-click-docking/ Have a nice docking! Robert Kiss CSO, mcule.com rkiss===mcule.com --- About mcule.com: DO EARLY PHASE DRUG DISCOVERY LIGHTENING FAST! Mcule.com is the online drug discovery platform. It offers a unique solution for pharma and biotech companies by providing molecular modelling tools and the highest quality purchasable compound database. Mcule.com is a market leader of online hit identification and lead optimization services. --e89a8f234ab1317c8404d11d2b02 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Molecular docking has never been easier!

Mcule.com, the online drug discovery platform, is pleased to an= nounce the release of the easiest molecular docking solution online: 1-Click Docking.

Draw a ligand, select a target, click on Dock and start browsing the re= sults!

Try 1-Click Docking now! It is FREE: https://mcule.com/apps/1-click-docking/<= br>
Have a nice docking!

Robert Kiss
CSO, mcule.com
rkiss===mcule.com

---

About mcule.com:
<= br> DO EARLY PHASE DRUG DISCOVERY LIGHTENING FAST!

Mcule.com is the onli= ne drug discovery platform. It offers a unique solution for pharma and biot= ech companies by providing molecular modelling tools and the highest qualit= y purchasable compound database. Mcule.com is a market leader of online hit= identification and lead optimization services.
--e89a8f234ab1317c8404d11d2b02-- From owner-chemistry@ccl.net Tue Dec 18 09:31:00 2012 From: "bonoit bonoit bonoit_10^yahoo.fr" To: CCL Subject: CCL: CBS extrapolation Message-Id: <-48005-121218092927-23506-CGPFO8wZmGzeJLkDWbCDdg,server.ccl.net> X-Original-From: "bonoit bonoit" Date: Tue, 18 Dec 2012 09:29:12 -0500 Sent to CCL by: "bonoit bonoit" [bonoit_10 : yahoo.fr] Dear CCLers, I'm using CBS methods in my research and i would like to know more about these methods. I'll be very grateful if you can explain me how the CBS extrapolation works, in other words how we obtain this quantity, and what is OIii? Other thing is, in CBS-4 we use more than 5 configurations and in CBS-Q more than 10 configurations in the CBS extrapolation step. My question is: what do you mean by configurations? Any help is appreciated With the best wishes Bonoit From owner-chemistry@ccl.net Tue Dec 18 10:17:00 2012 From: "bonoit bonoit bonoit_10:yahoo.fr" To: CCL Subject: CCL: Vibrational adiabatic barrier Message-Id: <-48006-121218101547-10656-uOoOD51suN1oDCLbTydlDw!A!server.ccl.net> X-Original-From: "bonoit bonoit" Date: Tue, 18 Dec 2012 10:15:45 -0500 Sent to CCL by: "bonoit bonoit" [bonoit_10+*+yahoo.fr] Dear CCLers, I'm writting to enquire about the vibrational adiabatic barrier. What does it mean and represent ? and what is the information that can we get from it? Thank you in advance Bonoit From owner-chemistry@ccl.net Tue Dec 18 19:51:00 2012 From: "Venable, Richard (NIH/NHLBI) E venabler(_)nhlbi.nih.gov" To: CCL Subject: CCL: protein ligand complex simulation on NAMD Message-Id: <-48007-121218190725-17719-mj8JHQVcTn/Wa/0d9T2G6A,,server.ccl.net> X-Original-From: "Venable, Richard (NIH/NHLBI) [E]" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 18 Dec 2012 19:06:53 -0500 MIME-Version: 1.0 Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler- -nhlbi.nih.gov] The ligand parameters should be chosen or prepared in a manner consistent with the protein force field (FF). If you are using the CHARMM protein FF, the www.paramchem.org site is the recommended pathway for adding ligand descriptions and parameters, in the context of the CHARMM General FF (CGenFF). Note also that the CHARMM protein FF has recently been updated to CHARMM36, the first major update since CHARMM22 was extended to become CHARMM22/CMAP (which some have mistakenly called CHARMM27). -- Rick Venable 5635 FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov On 12/18/12 3:51 AM, "Sobia A Halim sobia_halim]~[yahoo.com" wrote: > >Sent to CCL by: "Sobia A Halim" [sobia_halim|a|yahoo.com] >Dear All > >I am using NAMD for protein-ligand-membrane complex simulation. Please >anyone let me know how to generate ligand parameters and topology file. > >With best wishes and thanks in advance > >Sobia> > From owner-chemistry@ccl.net Tue Dec 18 21:36:00 2012 From: "Dimitrios Liakos dgliakos[#]googlemail.com" To: CCL Subject: CCL: CBS extrapolation Message-Id: <-48008-121218164314-7630-n27gLqdisGfbGe+aPpAM5Q_+_server.ccl.net> X-Original-From: Dimitrios Liakos Content-Type: multipart/alternative; boundary=f46d043d67e92268fa04d1276292 Date: Tue, 18 Dec 2012 22:43:07 +0100 MIME-Version: 1.0 Sent to CCL by: Dimitrios Liakos [dgliakos---googlemail.com] --f46d043d67e92268fa04d1276292 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Bonoit,**** ** ** We have recently described a new extrapolation scheme, based on the accuracy and efficiency of the LPNO-CCSD method, that produces results essentially identical with the CCSD(T)/CBS limit but in a much more efficient way. Please see for further details: **** *Improved Correlation Energy Extrapolation Schemes Based on Local Pair Natural Orbital Methods***** Dimitrios G. Liakos and Frank Neese**** The Journal of Physical Chemistry A 2012 116 (19), 4801-4816**** ** ** LPNO-CCSD method is implemented in the freely distributed quantum chemistry program ORCA. (http://www.mpibac.mpg.de/bac/logins/neese/description.php)**** Kind Regards, Dimitrios --------------------------------------------------- Dr. Dimitrios G. Liakos Max-Planck Institut f=FCr Bioanorganische Chemie Stiftstr. 34-36 D-45470 M=FClheim an der Ruhr Germany Phone: 0049 208 306 3886 E-Mail: dgliakos[*]cec.mpg.de ----------------------------------------------------- On Tue, Dec 18, 2012 at 3:29 PM, bonoit bonoit bonoit_10^yahoo.fr < owner-chemistry[*]ccl.net> wrote: > > Sent to CCL by: "bonoit bonoit" [bonoit_10 : yahoo.fr] > Dear CCLers, > I'm using CBS methods in my research and i would like to know more about > these methods. > I'll be very grateful if you can explain me how the CBS extrapolation > works, in other words how we obtain this quantity, and what is OIii? > Other thing is, in CBS-4 we use more than 5 configurations and in CBS-Q > more than 10 configurations in the CBS extrapolation step. My question is= : > what do you mean by configurations? > Any help is appreciated > With the best wishes > Bonoit > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --f46d043d67e92268fa04d1276292 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Dear Bonoit,=

=A0

efficiency of the L= PNO-CCSD method,=A0that produces results essentially identical with the=A0<= /p>

CCSD(T)/CBS limit but in a much more efficient way. Please see for further = details:

=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0

Improved Correla= tion Energy Extrapolation Schemes Based on Local Pair Natural Orbital Metho= ds

Dimitrios G. Liakos= and Frank Neese

The Journal of Physical Chemistry A=A02012=A0116=A0(19), 4801-= 4816

=A0

LP= NO-CCSD method is implemented in the freely distributed quantum chemistry p= rogram ORCA.=A0

(<= a href=3D"http://www.mpibac.mpg.de/bac/logins/neese/description.php" target= =3D"_blank" style=3D"color:rgb(17,85,204)">http://www.mpibac.mpg.de/bac/log= ins/neese/description.php)


Kind Regards,
Dimitrios

---------------------------------------------------
Dr. Dimitrios G. Lia= kos
Max-Planck Institut f=FCr Bioanorganische Chemie
Stiftstr. 34-36<= br>D-45470 M=FClheim an der Ruhr
Germany
Phone: 0049=A0208 306 3886
E-Mail:=A0dgliakos[*]cec.mpg.de=
-----------------------------------------------------

=
On Tue, Dec 18, 2012 at 3:29 PM, bonoit bonoit b= onoit_10^yahoo.fr <owner-chemistry[*]c= cl.net> wrote:

Sent to CCL by: "bonoit =A0bonoit" [bonoit_10 : yahoo.fr]
Dear CCLers,
I'm using CBS methods in my research and i would like to know more abou= t these methods.
I'll be very grateful if you can explain me how the CBS extrapolation w= orks, in other words how we obtain this quantity, and what is OIii?
Other thing is, in CBS-4 we use more than 5 configurations and in CBS-Q mor= e than 10 configurations in the CBS extrapolation step. My question is: wha= t do you mean by configurations?
Any help is appreciated
With the best wishes
Bonoit



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