From owner-chemistry "-at-" ccl.net Mon Jul 25 15:47:00 2011 From: "neranjan perera neranjan007_+_gmail.com" To: CCL Subject: CCL:G: Problem in preparing a proper input geometry for ONIOM calculations Message-Id: <-45144-110725134634-11601-mDOhVA78g9bRXxIRDFDMQw]![server.ccl.net> X-Original-From: neranjan perera Content-Type: multipart/alternative; boundary=000325554c86e0675404a8e864c6 Date: Mon, 25 Jul 2011 13:46:24 -0400 MIME-Version: 1.0 Sent to CCL by: neranjan perera [neranjan007]![gmail.com] --000325554c86e0675404a8e864c6 Content-Type: text/plain; charset=ISO-8859-1 Hi Krati Joshi, It would be helpful if you have provided at least a part of the output file to look into the matter. But most probably during ONIOM calculations, in gaussian it uses additional internal coordinates, to aid the optimization. What I am guessing is one of those values might have come closer to the maximum value, eg: angle coming closer to 180. so you may want to look at the angle/dihedral/distance which has an unreasonable value and can ask the program not to consider it, using the modredundent keyword. (more infor can be found in the webpage) hope it helps. Neranjan On Mon, Jul 25, 2011 at 9:45 AM, Gkourmpis, Thomas Thomas.Gkourmpis++ borealisgroup.com wrote: > > Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis_._borealisgroup.com] > Joshi Hi > > The most common error people do when they're preparing ONIOM structures is > either in the definition of the High and low level structures or in the > connecting point between them. In Gaussian the program connects the two > sections (high and low) via a dummy atom/bond (hydrogen). This atom has to > be connected only to one atom and not more as the system cannot deal with > it. > > I'm sorry I cannot be of more use to you but you don't really provide any > information on how you're building the structure. Anyhow I would recommend > you go through the review papers on the method by the relevant group that > developed it as they're very good and they explain in detail how the method > works. > > Hope it helps > Thomas > > -----Original Message----- > > From: owner-chemistry+thomas.gkourmpis==borealisgroup.com:+:ccl.net[mailto: > owner-chemistry+thomas.gkourmpis==borealisgroup.com:+:ccl.net] On Behalf > Of Krati Joshi kjjulie.joshia/gmail.com > Sent: Monday, July 25, 2011 12:38 PM > To: Gkourmpis, Thomas > Subject: CCL: Problem in preparing a proper input geometry for ONIOM > calculations > > > Sent to CCL by: "Krati Joshi" [kjjulie.joshi%a%gmail.com] > Dear all, > I am working on Gausian 03 from last few months. Write > now i am working on ONIOM calculations but i am facing a serious > problem in it.Whenever i submit a job, it crashes after some time with > an error message "Error in internal coordinates". It shows that there > is some problem in my input geometry therefor i tried several times with > different geometries but still i am not able to fix the problem.so pls > suggest me if anybody knows how to prepare a proper input goemetry for > ONIOM calculations.It will be of great help to me. > Thanking You > Krati Joshi > Catalysis Division National Chemical laboratry,Dr. Homi Bhaba road Pune, > India. > Email,kjjulie.joshi-at-gmail.comhttp:// > www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThisEmail and any files transmitted with it are confidential and > intended solely for the use of the individual or the entity to whom > it is addressed. If you have received this Email by error, please > notify the sender and delete the material from any storage device. > Borealis extends no warranties and makes no representations as to > the accuracy or completeness of the information provided. It is the > customer's responsibility to inspect and test our products and > technical advice in order to satisfy itself as to the suitability > of the products and technical advice for the customer's particular > purpose.> > > -- Neranjan Perera Graduate Student --000325554c86e0675404a8e864c6 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Krati Joshi,
=A0=A0=A0 It would be helpful if you have provided at le= ast a part of the output file to look into the matter. But most probably du= ring ONIOM calculations, in gaussian it uses additional internal coordinate= s, to aid the optimization.
=A0=A0=A0 What I am guessing is one of those values might have come closer = to the maximum value,
eg: angle coming closer to 180.

so you may= want to look at the angle/dihedral/distance which has an unreasonable valu= e and can ask the program not to consider it, using the modredundent keywor= d. (more infor can be found in the webpage)

hope it helps.

Neranjan
=A0=A0

On Mon, Jul 25, 2011 at 9:45 AM, Gkourmpis, Thomas Thomas.Gkourmpis++= borealisgroup.com <owner-chemistry^ccl.net> wrote:

Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis_._borealisgroup.com]
Joshi Hi

The most common error people do when they're preparing ONIOM structures= is either in the definition of the High and low level structures or in the= connecting point between them. In Gaussian the program connects the two se= ctions (high and low) via a dummy atom/bond (hydrogen). This atom has to be= connected only to one atom and not more as the system cannot deal with it.=

I'm sorry I cannot be of more use to you but you don't really provi= de any information on how you're building the structure. Anyhow I would= recommend you go through the review papers on the method by the relevant g= roup that developed it as they're very good and they explain in detail = how the method works.

Hope it helps
Thomas

-----Original Message-----
> From: owner-chemistry+thomas.gkourmpis=3D=3Dborealisgroup.com:+:ccl.net [mailto:owner-chemistry+thomas.gkourmpis= =3D=3Dborealisgroup.com:+:ccl.= net] On Behalf Of Krati Joshi kjjulie.joshia/gmail.com
Sent: Monday, July 25, 2011 12:38 PM
To: Gkourmpis, Thomas
Subject: CCL: Problem in preparing a proper input geometry for ONIOM calcul= ations


Sent to CCL by: "Krati =A0Joshi" [kjjulie.joshi%a%gmail.com]
Dear all,
=A0 =A0 =A0 =A0 =A0 =A0I am working on Gausian 03 from last few months. Wr= ite
now i am working on ONIOM calculations but i am facing a serious
problem in it.Whenever i submit =A0a job, it crashes after some time with an error message "Error in internal coordinates". It shows that t= here
is some problem in my input geometry therefor i tried several times with different geometries but still i am not able to fix the problem.so pls =A0s= uggest me if anybody knows how to prepare a proper input goemetry for ONIOM= calculations.It will be of great help to me.
Thanking You
Krati Joshi
Catalysis Division National Chemical laboratry,Dr. Homi Bhaba road Pune, In= dia.
Email,kjjulie.joshi-at-gmail.comhttp://www.ccl.net/cgi-bin/ccl/send_= ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/s= pammers.txtThis Email and any files transmitted with it are confidentia= l and
intended solely for the use of the individual or the entity to whom
it is addressed. If you have received this Email by error, please
notify the sender and delete the material from any storage device.
Borealis extends no warranties and makes no representations as to
the accuracy or completeness of the information provided. It is the
customer's responsibility to inspect and test our products and
technical advice in order to satisfy itself as to the suitability
of the products and technical advice for the customer's particular
purpose.



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--
Neranjan Perera
Graduate Student

--000325554c86e0675404a8e864c6--