From owner-chemistry@ccl.net Thu Nov 19 06:37:01 2009 From: "Mahmoud A. A. Ibrahim m.ibrahim1982/./yahoo.com" To: CCL Subject: CCL: ONIOM optimization of Gold compound Message-Id: <-40714-091119063603-9939-o8CW68VLV4InJgBD5nYXWg-,-server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary="0-333936961-1258630548=:62486" Date: Thu, 19 Nov 2009 03:35:48 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim1982.[A].yahoo.com] --0-333936961-1258630548=:62486 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Roby According to your Route Section, you have asked for one layer calculation u= sing b3lyp/genecp. The problem is returned to defining the keywords and bas= is set. You have to change your route section to: # opt=3Dmodredundant oniom (b3lyp/genecp:uff) geom=3Dconnectivity Card Title Charge and Multiplicity (Molecular defenition in Z-matrix) ...... ... .. . C H O N S P Cl 0 LANL2DZ **** C H O N S P Cl 0 LANL2DZ ----------------------------------- Sorry, but you said you have Gold in your system, I couldn't see it when yo= u defined the ECP basis set. I have another comment, why do you use UFF force field? think twice before = using it. Check your system again. Sincerely; M. Ibrahim Mahmoud A. A. Ibrahim Current Address School of Chemistry, University of Manchester,=20 Oxford Road, Manchester, M13 9PL, United Kingdom. =20 Home Address =20 Chemistry Department, Faculty of Science,=20 Minia University,=20 Minia 61519,Egypt. Contact Information Email: m.ibrahim[A]compchem.net Email: m.ibrahim1982[A]yahoo.com Website: www.compchem.net Fax No.: +20862342601 =20 --- On Wed, 11/18/09, Roby Kurian Roby_Kurian^^umit.maine.edu wrote: > From: Roby Kurian Roby_Kurian^^umit.maine.edu Subject: CCL: ONIOM optimization of Gold compound To: "Ibrahim, Mahmoud A. A. " Date: Wednesday, November 18, 2009, 3:53 PM Sent to CCL by: "Roby Kurian" [Roby_Kurian=3D=3D=3Dumit.maine.edu] Hi, I was trying to optimize a Gold compound (Gold bonded to glutathione) using= ONIOM. There are two levels of theory being used, B3LYP/6-31+g(d) for high= er layer and UFF for lower layer. I have defined Gold atom using LANL2DZ-EC= P. Now the calculation has converged but all atoms (including those were in lo= wer mechanics layer) ended up in upper(quantum) layer. The input I gave was # opt=3Dmodredundant oniom (b3lyp)/genecp geom=3Dconnectivity (Name) (Molecular defenition in Z-matrix) C H O N S P Cl 6-31+g(d):uff **** (LANL2DZ ECP from EMSL=A0 Basis Set Exchange Library) So any suggestions for modifying the route so that all atoms stay in the de= fined lavel? Thanks and Regards Roby Kurian Dept. of Chemistry University of Maine -=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 --0-333936961-1258630548=:62486 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Roby
According to your Route Section,= you have asked for one layer calculation using b3lyp/genecp. The problem i= s returned to defining the keywords and basis set.
You have to change yo= ur route section to:

# opt=3Dmodredundant oniom (b3lyp/genecp:uff) g= eom=3Dconnectivity

Card Title

Charge and Multiplicity
(Mol= ecular defenition in Z-matrix)
......
...
..
.

C H O N S= P Cl 0
LANL2DZ
****

C H O N S P Cl 0
LANL2DZ


--= ---------------------------------

Sorry, but you said you have Gold = in your system, I couldn't see it when you defined the ECP basis set.
I = have another comment, why do you use UFF force field? think twice before us= ing it.
Check your system again.
Sincerely;
M. Ibrahim


=


Mahmoud A. A. Ibrahim
Current Add= ress
= School of Chemistry, University of Manchester,
Oxford Road, Manchester,= M13 9PL, United Kingdom.

= Home Address =
Chemistry Department, Faculty of Science,
= Minia University,
Minia 61519,Egypt.

Contact Information
Email: m.ibrahim[A]= compchem.net
Email: m.ibrahim1982[A]yahoo.com
Website: www.compchem.net=
Fax No.: +20862342601


--- O= n Wed, 11/18/09, Roby Kurian Roby_Kurian^^umit.maine.edu <owner-chemistry[A]c= cl.net> wrote:

From: Roby Kurian= Roby_Kurian^^umit.maine.edu <owner-chemistry[A]ccl.net>
Subject: CC= L: ONIOM optimization of Gold compound
To: "Ibrahim, Mahmoud A. A. -id#4= 2s-" <m.ibrahim1982[A]yahoo.com>
Date: Wednesday, November 18, 2009,= 3:53 PM


Sent to CCL by: "Roby Kurian" = [Roby_Kurian=3D=3D=3Dumit.maine.edu]
Hi,

I was trying to optimize= a Gold compound (Gold bonded to glutathione) using ONIOM. There are two le= vels of theory being used, B3LYP/6-31+g(d) for higher layer and UFF for low= er layer. I have defined Gold atom using LANL2DZ-ECP.

Now the calcul= ation has converged but all atoms (including those were in lower mechanics = layer) ended up in upper(quantum) layer.

The input I gave was
# opt=3Dmodredundant oniom (b3lyp)/genecp geom=3Dconnectivity

(Name)<= br>(Molecular defenition in Z-matrix)


C H O N S P Cl
6-31+g(d= ):uff
****

(LANL2DZ ECP from EMSL  Basis Set Exchange Librar= y)


So any suggestions for modifying the route so that all atoms = stay in the defined lavel?

Thanks and Regards

Roby Kurian
= Dept. of Chemistry
University of Maine



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