From chemistry-request@server.ccl.net Sun Oct 27 09:34:08 2002 Received: from dedalus.lcc.ufmg.br ([150.164.65.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9REY8v08241 for ; Sun, 27 Oct 2002 09:34:08 -0500 Received: from p333 (lcc-ip4.lcc.ufmg.br [150.164.65.203]) by dedalus.lcc.ufmg.br (8.9.3/8.9.3) with SMTP id LAA42610; Sun, 27 Oct 2002 11:31:28 -0300 Message-ID: <000d01bd165a$a8ba6ee0$cb41a496@p333> From: "=?iso-8859-1?Q?Andr=E9_M._de_Oliveira?=" To: "Donald Keidel" , References: <013f01c27d55$21f6cdb0$529c178a@dopetec> Subject: Re: CCL:thermodynamic integration Date: Thu, 1 Jan 1998 00:11:58 -0200 Organization: UFOP MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000A_01BD1649.E09C3840" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 This is a multi-part message in MIME format. ------=_NextPart_000_000A_01BD1649.E09C3840 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Dr. Keidel Try classical Dr. P. Kollman's article, "Free energy calculations: = Appications to Chemical and Biochemical Phenomena" Chem. Rev. (1993) 93, = 2395-2417. Regards, Andr=E9 Mauricio de Oliveira ------------------------------------------------------------------ N=FAcleo de Estudos em Qu=EDmica Medicinal Departamento de Qu=EDmica Universidade Federal de Minas Gerais VOICE: 55-31-499-5765 FAX: 55-31-499-5700 amolive@dedalus.lcc.ufmg.br www.qui.ufmg.br/~nequim ----- Original Message -----=20 From: Donald Keidel=20 To: chemistry@ccl.net=20 Sent: Saturday, October 26, 2002 11:06 PM Subject: CCL:thermodynamic integration Hello CCLers, =20 I am thinking of purchasing AMBER and using Gibbs to perform some = thermodynamic integration techniques. The manual, however, does not go = into too much theory regarding the TI technique used in AMBER and in = particular the equation that is actually integrated over the limits of = lambda. Does anyone know of a reference that may describe the technique = and equation in more detail. Also, does anyone know of research groups = that may have developed their own code to perform TI calculations? All = responses are appreciated. Thank you very much. =20 =20 = -------------------------------------------------------------------------= -------------------------------------- Donald J. Keidel University of California, Riverside Department of Biochemistry and Molecular Biology Riverside, CA 92521 phone: (909) 787-5493 fax: (909) 787-4434 dkeidel397@att.net webpage: = www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm =20 ------=_NextPart_000_000A_01BD1649.E09C3840 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Dr. Keidel
 
Try classical Dr. P. Kollman's article, = "Free=20 energy calculations: Appications to Chemical and Biochemical Phenomena" = Chem.=20 Rev. (1993) 93, 2395-2417.
 
Regards,
 
Andr=E9 Mauricio de=20 Oliveira
-------------------------------------------------------------= -----
N=FAcleo=20 de Estudos em Qu=EDmica Medicinal
Departamento de = Qu=EDmica
Universidade=20 Federal de Minas Gerais
VOICE: 55-31-499-5765
FAX: = 55-31-499-5700
amolive@dedalus.lcc.ufmg.br
www.qui.ufmg.br/~nequim
----- Original Message -----
From:=20 Donald Keidel=20
Sent: Saturday, October 26, = 2002 11:06=20 PM
Subject: CCL:thermodynamic=20 integration

Hello CCLers,
 
I am thinking of purchasing AMBER and = using Gibbs=20 to perform some thermodynamic integration techniques.  The = manual,=20 however, does not go into too much theory regarding the TI technique = used in=20 AMBER and in particular the equation that is actually integrated over = the=20 limits of lambda.  Does anyone know of a reference that may = describe the=20 technique and equation in more detail.  Also, does anyone know of = research groups that may have developed their own code to perform TI=20 calculations?  All responses are appreciated.  Thank you = very=20 much.
 
 
----------------------------------------------------------------= -----------------------------------------------
Donald=20 J. Keidel
University of California, Riverside
Department of = Biochemistry=20 and Molecular Biology
Riverside, CA 92521
phone:  (909)=20 787-5493
fax:  (909) 787-4434
dkeidel397@att.net
webpage: = .htm">www.biochemistry.ucr.edu/gru/gradstudents/don_keidel/index.htm=
 
 
------=_NextPart_000_000A_01BD1649.E09C3840-- From chemistry-request@server.ccl.net Sun Oct 27 18:54:02 2002 Received: from oc30.uni-paderborn.de ([131.234.240.90]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9RNs1v19530 for ; Sun, 27 Oct 2002 18:54:02 -0500 Received: (from ib@localhost) by oc30.uni-paderborn.de (SGI-8.9.3/8.9.3) id CAA40480; Sun, 27 Oct 2002 02:24:31 +0100 (CET) Date: Sun, 27 Oct 2002 02:24:31 +0100 (CET) Message-Id: <200210270124.CAA40480@oc30.uni-paderborn.de> X-Authentication-Warning: oc30.uni-paderborn.de: ib set sender to ib@oc30.uni-paderborn.de using -f From: Ingo Brunberg To: oliwalk@wam.umd.edu CC: chemistry@ccl.net In-reply-to: <5.1.1.6.0.20021025145414.00b26180@imap.wam.umd.edu> (message from olivier walker on Fri, 25 Oct 2002 15:14:18 -0700) Subject: Re: CCL:AutodockTools and libglx library References: <5.1.1.6.0.20021025145414.00b26180@imap.wam.umd.edu> You must not put the path to the library into the XF86Config file, just the module name. So it should read: Load "glx". In case it is not a typo: The Section is called "Module", not "Modules". Regards, Ingo Brunberg > Hi all, > > > I'm currently trying to install autodocktools under Linux Mandrake 8.0 but > when executing pmv, I always receive the same message : > > "TclError: Togl: X server has no OpenGL GLX extension > hit enter to continue" > > On the autodocktools web site it is recommended to install libglx library, > but it is already installed because I can find the following files: > > > > libglx.so.1.0...... in usr/X11R6/lib/modules/extensions/ > nvidia.... in usr/X11R6/lib/modules/drivers/ > > > So, I added the following lines in the XF86Config-4 file: > > in the Section"Modules" > Load "/usr/X11R6/lib/modules/extensions/libglx.so" with a > link to libglx.so.1.0...... > > in the Section "Device" > Driver "nvidia" > > > But when I launch PMV, only a small window opens and I receive the same > message. > > Perhaps, my XF86Config-4 file is not appropriate. > What did I wrong? > > Thank you in advance for your helpful advices > > > > ************************************************** > Olivier WALKER-Research Assistant > Department of Chemistry & Biochemistry > University of Maryland > College Park, MD 20742 > USA > ************************************************** > Fax : 301-314-0386 > Phone : 301-405-8710 > E-mail : oliwalk@wam.umd.edu > **************************************************