From owner-chemistry@ccl.net Fri Feb 26 07:48:01 2016 From: "Bulumoni Kalita bulumoni:dibru.ac.in" To: CCL Subject: CCL:G: SCF convergence problem with M06L functional in Gaussian 09 Message-Id: <-52051-160226001221-7617-fFz6YrRz0kX+/THD21KhBg|-|server.ccl.net> X-Original-From: "Bulumoni Kalita" Date: Fri, 26 Feb 2016 00:12:19 -0500 Sent to CCL by: "Bulumoni Kalita" [bulumoni- -dibru.ac.in] Dear CCL users, I have optimized tetrahedral structure of Pd4 cluster in (UB3LYP/LANL2DZ) level in Gaussian 09. I wanted to repeat the calculation in (UM06L/LANL2DZ) level. However, SCF is not converging in this case. Rather it is fluctuating between to range of values. I have tried using SCF(xqc, maxcycle=500), opt(maxcycle=500) etc. Please give your valuable suggestions to overcome this problem. From owner-chemistry@ccl.net Fri Feb 26 08:23:01 2016 From: "Yujun Zhu 675096471 a qq.com" To: CCL Subject: CCL: virtual atoms in materials studio interface Message-Id: <-52052-160226023718-21195-sIMjB+Mc3DGHage0W2kuFQ]![server.ccl.net> X-Original-From: "Yujun Zhu" <675096471---qq.com> Date: Fri, 26 Feb 2016 02:37:17 -0500 Sent to CCL by: "Yujun Zhu" [675096471#,#qq.com] I want to build virtual atoms in materials studio interface used in sorption module for GCMC simulation, someone said that this can be done by setting the mass of atom as zero. Have anyone done this procedure before? From owner-chemistry@ccl.net Fri Feb 26 08:58:01 2016 From: "Yujun Zhu 675096471()qq.com" To: CCL Subject: CCL: virtual atoms in materials studio interface Message-Id: <-52053-160226024312-21545-O8BSmktvogsWpaNpAgftdA]*[server.ccl.net> X-Original-From: "Yujun Zhu" <675096471(a)qq.com> Date: Fri, 26 Feb 2016 02:43:10 -0500 Sent to CCL by: "Yujun Zhu" [675096471 _ qq.com] I want to build virtual atoms in materials studio interface used in sorption module for GCMC simulation, someone said that this can be done by setting the mass of atom as zero. Have anyone done this procedure before? From owner-chemistry@ccl.net Fri Feb 26 09:32:00 2016 From: "Guzman, Francisco fg58:_:njit.edu" To: CCL Subject: CCL:G: SCF convergence problem with M06L functional in Gaussian 09 Message-Id: <-52054-160226083122-16482-tOdoSaJWM2tTwT+CjKzFxA.:.server.ccl.net> X-Original-From: "Guzman, Francisco" Content-Type: multipart/alternative; boundary=001a114a839e4ab73c052cac5008 Date: Fri, 26 Feb 2016 08:31:16 -0500 MIME-Version: 1.0 Sent to CCL by: "Guzman, Francisco" [fg58/./njit.edu] --001a114a839e4ab73c052cac5008 Content-Type: text/plain; charset=UTF-8 What is the error? Error termination L9999? Can you post your input file as well. On Fri, Feb 26, 2016 at 12:12 AM, Bulumoni Kalita bulumoni:dibru.ac.in < owner-chemistry- -ccl.net> wrote: > > Sent to CCL by: "Bulumoni Kalita" [bulumoni- -dibru.ac.in] > Dear CCL users, > I have optimized tetrahedral structure of Pd4 cluster in > (UB3LYP/LANL2DZ) level in Gaussian 09. I wanted to repeat the calculation > in (UM06L/LANL2DZ) level. However, SCF is not converging in this case. > Rather it is fluctuating between to range of values. I have tried using > SCF(xqc, maxcycle=500), opt(maxcycle=500) etc. > > Please give your valuable suggestions to overcome this problem.> > > -- Francisco Guzman PhD Candidate Otto H. York Department of Chemical, Biological and Pharmaceutical Engineering New Jersey Institute of Technology Email: fg58- -njit.edu, guzman.research- -gmail.com Cell: 347-806-3977 --001a114a839e4ab73c052cac5008 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
What is the error? Error termination L9999? Can you post y= our input file as well.

On Fri, Feb 26, 2016 at 12:12 AM, Bulumoni Kalita bulumoni= :dibru.ac.in <owner-chemistry- -ccl= .net> wrote:

Sent to CCL by: "Bulumoni=C2=A0 Kalita" [bulumoni- -dibru.ac.in]
Dear CCL users,
=C2=A0 =C2=A0 =C2=A0 =C2=A0I have optimized tetrahedral structure of Pd4 cl= uster in (UB3LYP/LANL2DZ) level in Gaussian 09. I wanted to repeat the calc= ulation in (UM06L/LANL2DZ) level.=C2=A0 However, SCF is not converging in t= his case.=C2=A0 Rather it is fluctuating between to range of values.=C2=A0 = I have tried using SCF(xqc, maxcycle=3D500), opt(maxcycle=3D500) etc.

Please give your valuable suggestions to overcome this problem.



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--
F= rancisco Guzman
PhD Candidate
Otto H. York D= epartment of Chemical, Biological and Pharmaceutical Engineering
New Jer= sey Institute of Technology
--001a114a839e4ab73c052cac5008-- From owner-chemistry@ccl.net Fri Feb 26 10:07:01 2016 From: "Close, David M. CLOSED!^!mail.etsu.edu" To: CCL Subject: CCL:G: SCF convergence problem with M06L functional in Gaussian 09 Message-Id: <-52055-160226085909-24009-Wp/aX4ZPCg09JUG878iW+w:-:server.ccl.net> X-Original-From: "Close, David M." Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 26 Feb 2016 13:58:59 +0000 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED : mail.etsu.edu] Bulumoni: If the solution is oscillating, then adding more cycles will not help. It would be best to animate the output and see which part of the molecule is changing. Usually this is evident. Perhaps some rocking motion. Anyway, find the atoms involved and freeze their motion. Then the optimization will converge rapidly. Regards, Dave Close. -----Original Message----- > From: owner-chemistry+closed==etsu.edu . ccl.net [mailto:owner-chemistry+closed==etsu.edu . ccl.net] On Behalf Of Bulumoni Kalita bulumoni:dibru.ac.in Sent: Friday, February 26, 2016 12:12 AM To: Close, David M. Subject: CCL:G: SCF convergence problem with M06L functional in Gaussian 09 Sent to CCL by: "Bulumoni Kalita" [bulumoni- -dibru.ac.in] Dear CCL users, I have optimized tetrahedral structure of Pd4 cluster in (UB3LYP/LANL2DZ) level in Gaussian 09. I wanted to repeat the calculation in (UM06L/LANL2DZ) level. However, SCF is not converging in this case. Rather it is fluctuating between to range of values. I have tried using SCF(xqc, maxcycle=500), opt(maxcycle=500) etc. Please give your valuable suggestions to overcome this problem.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Feb 26 13:34:01 2016 From: "Suriti Sachdewa suritisachdewa^-^gmail.com" To: CCL Subject: CCL: Hyperpolarizability of Pervoskite Message-Id: <-52056-160226125625-1764-d2LhoMfVt2MaaWM/C93Jsw * server.ccl.net> X-Original-From: "Suriti Sachdewa" Date: Fri, 26 Feb 2016 12:56:24 -0500 Sent to CCL by: "Suriti Sachdewa" [suritisachdewa^^^gmail.com] Hello, I am new to computational Chemistry. Can anyone please tell me that which software can we use to calculate first hyperpolarizabilities of pervoskite materials? Thanks in Advance ! From owner-chemistry@ccl.net Fri Feb 26 16:06:01 2016 From: "=?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal victor]~[fluor.quimica.uniovi.es" To: CCL Subject: CCL: SCF convergence problem with M06L functional in Gaussian 09 Message-Id: <-52057-160226154439-2331-ZsxcWKXTt4YFD/so/1XTvA-,-server.ccl.net> X-Original-From: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal Content-disposition: inline Content-transfer-encoding: 8BIT Content-type: text/plain; charset=iso-8859-1 Date: Fri, 26 Feb 2016 21:12:50 +0100 MIME-version: 1.0 Sent to CCL by: =?iso-8859-1?Q?V=EDctor_Lua=F1a?= Cabal [victor]![fluor.quimica.uniovi.es] On Fri, Feb 26, 2016 at 01:58:59PM +0000, Close, David M. CLOSED!^!mail.etsu.edu wrote: > > Sent to CCL by: "Close, David M." [CLOSED : mail.etsu.edu] > Bulumoni: > If the solution is oscillating, then adding more cycles will not help. It would be best to animate the output and see which part of the molecule is changing. Usually this is evident. Perhaps some rocking motion. Anyway, find the atoms involved and freeze their motion. Then the optimization will converge rapidly. Dave's solution is best, but damping the scf convergence may require less user time and more cpu time if you are in a hurry. Good luck, Víctor Luaña -- . . "The hardest part in solving a problem is recognizing / `' \ its existence. Learning the causes CAN be the road to /(o)(o)\ the solution." /`. \/ .'\ -- ¿? / '`'` \ "Lo mediocre es peor que lo bueno, pero también es peor | \'`'`/ | que lo malo, porque la mediocridad no es un grado, es una | |'`'`| | actitud" \/`'`'`'\/ -- Jorge Wasenberg, 2015 ===(((==)))==================================+========================= ! Dr.Víctor Luaña, in silico chemist & prof. ! Mediocre is worse than ! Departamento de Química Física y Analítica ! good, but it is also ! Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because ! e-mail: victor^fluor.quimica.uniovi.es ! mediocrity is not a grade, ! phone: +34-985-103491 fax: +34-985-103125 ! it is an attitude +--------------------------------------------+ GroupPage : http://azufre.quimica.uniovi.es/ (being reworked) From owner-chemistry@ccl.net Fri Feb 26 18:01:00 2016 From: "Scott Brozell srb|osc.edu" To: CCL Subject: CCL: Can Dock6.7 predict binding site? Message-Id: <-52058-160226175746-18530-QTSK6M3f/1F8NgNs+FMNPg===server.ccl.net> X-Original-From: Scott Brozell Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Fri, 26 Feb 2016 17:57:36 -0500 Mime-Version: 1.0 Sent to CCL by: Scott Brozell [srb^osc.edu] Hi, Short answers to your questions are 1. you identified the binding region(s); this could have been a single specific site or the whole receptor; see this tutorial for the recipe: http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm 2. Dock can be used to predict binding sites, but that is not its main intended purpose nor a particular strength. 3. Dock's main focus is receptor-ligand complexes. Novel uses have been made in the past. For some more detail about binding site selection, see the response on the Dock mailing list: http://mailman.docking.org/pipermail/dock-fans/2016-February/003150.html For an overview of Dock, see http://dock.compbio.ucsf.edu/Overview_of_DOCK/index.htm scott On Thu, Feb 25, 2016 at 02:31:12AM -0500, Syeda Sumayya Tariq sumayyatariq7**gmail. com wrote: > > I have recently started working with Dock6.7 and have a little query. > The issue is I have used Dock6.7 to dock a receptor protein with a small > molecule I retrieved from a database. The receptor site where docking > occurred shows some of the residues SAME as were predicted CPORT which is > responsible for predicting active residues. > My question is how did Dock identify the binding site? Is it by chance or > is Dock able to predict binding site also? Is it true that Dock can only > work with a receptor-ligand complex? From owner-chemistry@ccl.net Fri Feb 26 18:35:01 2016 From: "Vijay Singh Parmar vsparmar(_)iiserb.ac.in" To: CCL Subject: CCL:G: DFT, Broken-symmetry on MOF Message-Id: <-52059-160226102739-5317-ZwLwkEEX84pIn/wNYsdY1A+/-server.ccl.net> X-Original-From: Vijay Singh Parmar Content-Type: multipart/alternative; boundary=94eb2c03588c261faa052cadf019 Date: Fri, 26 Feb 2016 20:57:04 +0530 MIME-Version: 1.0 Sent to CCL by: Vijay Singh Parmar [vsparmar(-)iiserb.ac.in] --94eb2c03588c261faa052cadf019 Content-Type: text/plain; charset=UTF-8 Respected computational chemists, I am a beginner at computational chemistry. I want to perform a broken-symmetry calculation in order to find the exchange interactions in my Dy-MOF(metal-organic frameworks) Using gaussian09 or ORCA or ADF. I tried for a Di-nuclear complex but i dont get how to do the same for a MOF, should i use the assymetric unit only or more number of atoms somehow? please help! Thanks in advance Vijay Singh Parmar Department of Chemistry Contact: +91-9691888500 IISER Bhopal Bhouri --94eb2c03588c261faa052cadf019 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Respected computational chemists,

I am a beginner a= t computational chemistry.
=C2=A0
I want to perform a broken-symmetr= y calculation in order to find the exchange interactions in my Dy-MOF(metal= -organic frameworks) Using gaussian09 or ORCA or ADF. I tried for a Di-nucl= ear complex but i dont get how to do the same for a MOF, should i use the a= ssymetric unit only or more number of atoms somehow?

please help! Th= anks in advance


<= div dir=3D"ltr">
=
Vijay Singh Parma= r
<= font size=3D"2">Department of Chemistry=C2=A0
Contact: +91-9691888500IISER Bhopal
=
Bhouri
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