From owner-chemistry@ccl.net Sun Jun 14 06:52:01 2009 From: "salah said m-22[]hotmail.fr" To: CCL Subject: CCL:G: fix dihedral angle Message-Id: <-39506-090614064448-6451-pHZjM1MD3nrg5jtt5OusFg[a]server.ccl.net> X-Original-From: "salah said" Date: Sun, 14 Jun 2009 06:44:45 -0400 Sent to CCL by: "salah said" [m-22..hotmail.fr] Hi, What is the best method to fix:restraint a dihedral angle during optimisation with gaussian. Thanks From owner-chemistry@ccl.net Sun Jun 14 07:27:01 2009 From: "salah said m-22*_*hotmail.fr" To: CCL Subject: CCL:G: percentage distribution of the potential energy Message-Id: <-39507-090614065105-6874-qqGb/l9X8qiULCtcxl61fw=-=server.ccl.net> X-Original-From: "salah said" Date: Sun, 14 Jun 2009 06:51:02 -0400 Sent to CCL by: "salah said" [m-22.##.hotmail.fr] Hi, How to calculate with gaussian03 the percentage distribution of the potential energy in terms of normal modes of vibration??? Thanks. From owner-chemistry@ccl.net Sun Jun 14 08:04:01 2009 From: "Mahmoud A. A. Ibrahim m.ibrahim1982++yahoo.com" To: CCL Subject: CCL:G: fix dihedral angle Message-Id: <-39508-090614074057-2765-ZThP2BQfYlJGtkpeJ/XzLA#%#server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary="0-315318881-1244979646=:81079" Date: Sun, 14 Jun 2009 04:40:46 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim1982|yahoo.com] --0-315318881-1244979646=:81079 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Salah You can use Modredundant keyword in the rout section (i.e. Opt=3DModredunda= nt) and after the molecule coordinates and variable, you should write: atom1 atom2 atom3 atom4 F where atom1,2,3 and 4 are your atom number for them you are freezing the di= hedral angle among them. For more information, have a look on Gaussian website, http://www.gaussian.= com/g_tech/g_ur/k_opt.htm Sincerely; M. Ibrahim Mahmoud A. A. Ibrahim Current Address School of Chemistry, University of Manchester,=20 Oxford Road, Manchester, M13 9PL, United Kingdom. Mahmoud.Ibrahim-2(0)postgrad.manchester.ac.uk=20 =20 Home Address =20 Chemistry Department, Faculty of Science,=20 Minia University,=20 Minia 61519,Egypt.=20 M.Ibrahim1982(0)yahoo.com=20 Mobile Phone No.: +20102554083 =20 Land Phone No.: +20226635916=20 Fax No.: +20862342601 --- On Sun, 6/14/09, salah said m-22[]hotmail.fr = wrote: > From: salah said m-22[]hotmail.fr Subject: CCL:G: fix dihedral angle To: "Ibrahim, Mahmoud A. A. " Date: Sunday, June 14, 2009, 11:44 AM Sent to CCL by: "salah=A0 said" [m-22..hotmail.fr] Hi, What is the best method to fix:restraint a dihedral angle during optimisati= on with gaussian. Thanks -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A=0A --0-315318881-1244979646=:81079 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Salah
You can use Modredundant keywor= d in the rout section (i.e. Opt=3DModredundant) and after the molecule coor= dinates and variable, you should write:
atom1 atom2 atom3 atom4 F
whe= re atom1,2,3 and 4 are your atom number for them you are freezing the dihed= ral angle among them.
For more information, have a look on Gaussian webs= ite, http://www.gaussian.com/g_tech/g_ur/k_opt.htm
Sincerely;
M. Ibra= him

Mahmoud A. A. Ibrahim

Current Address
School of Chemistry, University of= Manchester,
Oxford Road, Manchester, M13 9PL, United Kingdom.
Mahmoud.Ibrahim-2(0)postgrad.manchester.ac.uk

= Home Address
Chemistry Department, = Faculty of Science,
Minia University,
Mi= nia 61519,Egypt.
M.Ibrahim1982(0)yahoo.com
Mobile Phon= e No.: +20102554083
La= nd Phone No.: +20226635916
Fax No.: +20862342601
=

--- On Sun, 6/14/09, salah said m-22[]hotmail.fr <owner-ch= emistry(0)ccl.net> wrote:

From: sa= lah said m-22[]hotmail.fr <owner-chemistry(0)ccl.net>
Subject: CCL:G= : fix dihedral angle
To: "Ibrahim, Mahmoud A. A. " <m.ibrahim1982(0)yahoo.com>
Date: Sunday, June 14, 2009, 11:44 AM

Sent to CCL by: "salah  said" [m-22= ..hotmail.fr]
Hi,
What is the best method to fix:restraint a dihedral= angle during optimisation with gaussian.
Thanks



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=0A=0A --0-315318881-1244979646=:81079-- From owner-chemistry@ccl.net Sun Jun 14 19:27:00 2009 From: "james peter jp07:+:sify.com" To: CCL Subject: CCL: How to select protien for docking Message-Id: <-39509-090614081415-26852-8qW4va+Oe/qbU1MzDUodJw(a)server.ccl.net> X-Original-From: "james peter" Date: Sun, 14 Jun 2009 08:14:11 -0400 Sent to CCL by: "james peter" [jp07,sify.com] Hi, My work is on synthetic chemistry. I have synthesized a series of biologically activ compounds. just I want to perform protien ligand docking taking my molecules as ligand. My problem is how can I select a protien and from where I can download a protien. I have read many tutorials describing method of docking taking an example protien and ligand. but my problem is how to select a protien from a wide list of protien structures and how to fit ligand structure into protine for docking. Please help me so that I can perform docking. Thanking in advance J.Peter From owner-chemistry@ccl.net Sun Jun 14 22:02:01 2009 From: "Henry Martinez hmartine . gmail.com" To: CCL Subject: CCL: coupling constants explanation Message-Id: <-39510-090614215849-7054-EWczmJ5prg3hlF3oD9C7tg**server.ccl.net> X-Original-From: "Henry Martinez" Date: Sun, 14 Jun 2009 21:58:45 -0400 Sent to CCL by: "Henry Martinez" [hmartine(0)gmail.com] I am organic chemist, and I would highly appreciate if anybody define in ORGANIC CHEMISTRY WORDS (or the next easiest way to understand) the next 4 terms, the all related with the calculation of coupling constants. Fermi Contact (FC) Spin-dipolar (SD) Paramagnetic spin-orbit (PSO) Diamagnetic spin-orbit (DSO) Thanks a lot