From owner-chemistry@ccl.net Sun Mar 7 03:19:01 2010 From: "a/yahoo.com" To: CCL Subject: CCL:G: G03:ONIOM /Surface Message-Id: <-41385-100307030603-8119-6sXkud2z1eAQSu4OJYRHSQ..server.ccl.net> X-Original-From: ahoo.com> Content-Type: multipart/alternative; boundary="0-455834283-1267945796=:71280" Date: Sat, 6 Mar 2010 23:09:56 -0800 (PST) MIME-Version: 1.0 Sent to CCL by:^yahoo.com] --0-455834283-1267945796=:71280 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Thank you all for your suggestions. I have tried ONIOM with the following line in the route section. However th= is does not generate any surface (HOMO) in gaussview when opening the check= point file. What is wrong ? ***************************************************************************= **** #p oniom(uhf/sto-3g*:uhf/sto-3g*)=A0 nosymm=A0 charge 1 2 1 2 1 2=A0 ; two molecules with unity charge on each=20 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 ; Molecule structure with = two layers H & L point charges=20 ***************************************************************************= **** Thanks a lot. AR --- On Tue, 3/2/10, Morad El-Hendawy m80elhendawy a yahoo.com wrote: > From: Morad El-Hendawy m80elhendawy a yahoo.com Subject: CCL:G: G03:Different Charges on Molecules To: "yahoo.com> Date: Tuesday, March 2, 2010, 6:42 PM Hi Try your calculations with ONIOM (QM/QM). It may be helpful in your case. Regards, Morad --- On Tue, 3/2/10, D!yahoo.com wrote: > From: =3D!yahoo.com Subject: CCL:G: G03:Different Charges on Molecules To: "El-Hendawy, Morad Metwally " Date: Tuesday, March 2, 2010, 4:11 PM Dear CCL subscribers, I have two molecules near each other. How can I assign different amount of = charges to each molecule in Gaussian 03? Thanks in advance. Regards, AF =0A=0A =20 =0A=0A =0A=0A=0A --0-455834283-1267945796=:71280 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Thank you all for your suggestions.
I have= tried ONIOM with the following line in the route section. However this doe= s not generate any surface (HOMO) in gaussview when opening the checkpoint = file. What is wrong ?

**********************************************= *********************************
#p oniom(uhf/sto-3g*:uhf/sto-3g*) = ; nosymm  charge

1 2 1 2 1 2  ; two molecules with unity c= harge on each

         = ;        ; Molecule structure with two l= ayers H & L
point charges
**************************************= *****************************************

Thanks a lot.
AR
--- On Tue, 3/2/10, Morad El-Hendawy m80elhendawy a yahoo.com <ow= ner-chemistry,,ccl.net> wrote:

From= : Morad El-Hendawy m80elhendawy a yahoo.com <owner-chemistry,,ccl.net>=
Subject: CCL:G: G03:Different Charges on Molecules
To: "yahoo.com>
Date: Tuesday, March 2, 2010= , 6:42 PM

Hibr>Try your calcula= tions with ONIOM (QM/QM). It may be helpful in your case.
Regards,
Mo= rad

--- On Tue, 3/2/10, =3D!yahoo.com= <owner-chemistry%%ccl.net> wrote:

From: 3D!yahoo.com <owner-chemis= try%%ccl.net>
Subject: CCL:G: G03:Different Charges on Molecules
T= o: "El-Hendawy, Morad Metwally " <m80elhendawy%%yahoo.com>
Date: T= uesday, March 2, 2010, 4:11 PM

Dear CCL subscribers,
I have two = molecules near each other. How can I assign different amount of charges to = each molecule in Gaussian 03?
Thanks in advance.
Regards,
AF

=0A=0A

=0A=0A

=0A=0A = --0-455834283-1267945796=:71280-- From owner-chemistry@ccl.net Sun Mar 7 10:56:01 2010 From: "keetch keetch keeetch ~~ yahoo.com" To: CCL Subject: CCL: Cp-M-Cp bond angle Message-Id: <-41386-100307012325-23468-E5tY7DZ828U7hiJNIq1vMQ=-=server.ccl.net> X-Original-From: keetch keetch Content-Type: multipart/alternative; boundary="0-914359209-1267942991=:46617" Date: Sat, 6 Mar 2010 22:23:11 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: keetch keetch [keeetch a yahoo.com] --0-914359209-1267942991=:46617 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Radek and Pablo, =A0=A0 Thank you very much for your valuable suggestion.=A0 Yes, I can do i= t with PLATON. Thanks a lot. krishna. --- On Sun, 7/3/10, Pablo Vitoria Garcia qibvigap]_[lg.ehu.es wrote: > From: Pablo Vitoria Garcia qibvigap]_[lg.ehu.es Subject: CCL: Cp-M-Cp bond angle To: "Bellie, Krishnamoorthy Sundaram " Date: Sunday, 7 March, 2010, 2:02 AM Sent to CCL by: Pablo Vitoria Garcia [qibvigap++lg.ehu.es] Hi, PLATON will indeed recognize all ferrocene-like fragments without user inpu= t, and will calculate automatically the Cp ring centroids, distances from t= he centroids to the metal, the angle centroid1-M-centroid2, and much more. But I don't know if it accepts .xyz files as input, although you could tran= form them to pdb or another formats easily. Cheers Pablo "Radoslaw Kaminski rkaminski.rk,,gmail.com" ha = escrito: > Hi, >=20 > I'm a crystallographer but programs like Diamond, PLATON or maybe Mercury > can do it very easily. I use Diamond 3 and it can read different types of > files like e.g. XYZ ones so it can be used also with theoretical data. > Mercury also. I'm sure there are lots of such programs. Is this answer yo= ur > question at least partially? I don't know programs which could recognize = Cp > rings automatically and calculate appropriate angles, unfortunately. >=20 > Cheers, >=20 > Radek >=20 >=20 > 2010/3/5 keetch keetch keeetch^^yahoo.com >=20 >> Dear CCL members, >>=20 >>=A0 =A0=A0=A0I have calculated the centroids and got the angle. I have se= nt the post >> to know whether it is possible to get the Cg-M-Cg angle directly from an= y >> programmes, which can calculate the centroids automatically. I am sorry = for >> the inconvenience. >>=20 >> Krishna >>=20 >>=20 >> --- On *Fri, 5/3/10, Radoslaw Kaminski rkaminski.rk(!)gmail.com >> * wrote: >>=20 >>=20 >> From: Radoslaw Kaminski rkaminski.rk(!)gmail.com > > >> Subject: CCL: Cp-M-Cp bond angle >> To: "Bellie, Krishnamoorthy Sundaram " >> Date: Friday, 5 March, 2010, 8:22 PM >>=20 >> Hi, >>=20 >> What does it mean to view? You can calculate the centroids and than the >> angle. I don't understand the problem to be honest... >>=20 >> Cheers, >>=20 >> Radek >>=20 >> 2010/3/5 Krishna B S bskimo*|*gmail.com >> > >>=20 >>>=20 >>> Sent to CCL by: "Krishna B S" [bskimo_._gmail.com] >>> Dear CCL Members, >>>=20 >>>=A0 Can anyone tell me, how to view the Cp(centroid)-M-Cp(centroide) Bon= d >>> Angle from the optimized geometry?... >>>=20 >>> Thanks in advance... >>>=20 >>> krishna>> >>> E-mail to subscribers: CHEMISTRY++ccl.netor use:>> >>> E-mail to administrators: CHEMISTRY-REQUEST++ccl.netor use>> >>>=20 >>>=20 >>=20 >> ------------------------------ >> The INTERNET now has a personality. YOURS! See your Yahoo! Homepage >> . >=20 --******************************** Pablo Vitoria Garcia Servicios Generales de Rayos X Universidad del Pa=EDs Vasco (UPV/EHU) Fac. Ciencia y Tecnolog=EDa, Edificio CD3 c/ Barrio Sarriena s/n, 48940 Leioa (Bizkaia) Tfno. +34 946015334 Fax=A0=A0=A0+34 946013500 ******************************** -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0=A0=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message=A0 =A0=A0=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message=A0 =A0=A0=A0http://www.ccl.net/chemistry/sub_unsub.shtml=A0 =A0=A0=A0http://www.ccl.net/spammers.txt=0A=0A=0A The INTERNET now has a personality. YOURS! See your Yahoo! H= omepage. http://in.yahoo.com/ --0-914359209-1267942991=:46617 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Radek and Pablo,

   Tha= nk you very much for your valuable suggestion.  Yes, I can do it with = PLATON.

Thanks a lot.

krishna.

--- On Sun, 7/3/10, = Pablo Vitoria Garcia qibvigap]_[lg.ehu.es <owner-chemistry ~~ ccl.net>= ; wrote:

From: Pablo Vitoria Garcia= qibvigap]_[lg.ehu.es <owner-chemistry ~~ ccl.net>
Subject: CCL: Cp-M= -Cp bond angle
To: "Bellie, Krishnamoorthy Sundaram " <keeetc= h ~~ yahoo.com>
Date: Sunday, 7 March, 2010, 2:02 AM


Sent to CCL by: Pablo Vitoria Garcia [qibvigap++lg.ehu.e= s]
Hi,

PLATON will indeed recognize all ferrocene-like fragments = without user input, and will calculate automatically the Cp ring centroids, distances from the centroids to the metal, the angle centroid1-M-centroid2= , and much more.
But I don't know if it accepts .xyz files as input, alt= hough you could tranform them to pdb or another formats easily.

Chee= rs

Pablo

"Radoslaw Kaminski rkaminski.rk,,gmail.com" <owne= r-chemistry^-^ccl.net> ha escrito:

> Hi,
>
> I'm = a crystallographer but programs like Diamond, PLATON or maybe Mercury
&g= t; can do it very easily. I use Diamond 3 and it can read different types o= f
> files like e.g. XYZ ones so it can be used also with theoretical = data.
> Mercury also. I'm sure there are lots of such programs. Is th= is answer your
> question at least partially? I don't know programs w= hich could recognize Cp
> rings automatically and calculate appropria= te angles, unfortunately.
>
> Cheers,
>
> Radek>
>
> 2010/3/5 keetch keetch keeetch^^yahoo.com <owner-chemistry],[ccl.net>
>
>> Dear CCL members,>>
>>     I have calculated the centr= oids and got the angle. I have sent the post
>> to know whether it= is possible to get the Cg-M-Cg angle directly from any
>> program= mes, which can calculate the centroids automatically. I am sorry for
>= ;> the inconvenience.
>>
>> Krishna
>>
&= gt;>
>> --- On *Fri, 5/3/10, Radoslaw Kaminski rkaminski.rk(!)= gmail.com
>> <owner-chemistry||ccl.net>* wrote:
>> =
>>
>> From: Radoslaw Kaminski rkaminski.rk(!)gmail.com = <owner-chemistry||ccl.net
>> >
>> Subject: CCL: Cp-= M-Cp bond angle
>> To: "Bellie, Krishnamoorthy Sundaram " <keee= tch||yahoo.com>
>> Date: Friday, 5 March, 2010, 8:22 PM
>= >
>> Hi,
>>
>> What does it mean to view? You can calculate the centroids and than the
>> angle. I do= n't understand the problem to be honest...
>>
>> Cheers,=
>>
>> Radek
>>
>> 2010/3/5 Krishna B= S bskimo*|*gmail.com <owner-chemistry++ccl.net<http://in.mc244.mail.yahoo.com/mc/compose?to=3Downer-chemistry++ccl.n= et>
>> >
>>
>>>
>>> S= ent to CCL by: "Krishna B S" [bskimo_._gmail.com]
>>> Dear CCL = Members,
>>>
>>>  Can anyone tell me, how to = view the Cp(centroid)-M-Cp(centroide) Bond
>>> Angle from the o= ptimized geometry?...
>>>
>>> Thanks in advance...=
>>>
>>> krishna>>
>>> E-mail to= subscribers: CHEMISTRY++ccl.net<http://in.mc244.mail.yahoo.com/mc/compose?to=3DCHEMISTRY= ++ccl.net>or use:>>
>>> E-mail to administrators: = CHEMISTRY-REQUEST++ccl.net<http://in.mc244.= mail.yahoo.com/mc/compose?to=3DCHEMISTRY-REQUEST++ccl.net>or use>= >
>>>
>>>
>>
>> -----------= -------------------
>> The INTERNET now has a personality. YOURS! = See your Yahoo! Homepage<http://in.rd.yahoo.com/tagline_yy= i_1/*http://in.yahoo.com/>
>> .
>



--*= *******************************
Pablo Vitoria Garcia
Servicios Genera= les de Rayos X
Universidad del Pa=EDs Vasco (UPV/EHU)
Fac. Ciencia y = Tecnolog=EDa, Edificio CD3
c/ Barrio Sarriena s/n, 48940 Leioa (Bizkaia)
Tfno. +34= 946015334
Fax   +34 946013500
***********************= *********



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=0AThe INTERNET now has a personality. YOURS! See your Yah= oo! Homepage. --0-914359209-1267942991=:46617--