From owner-chemistry@ccl.net Tue Dec 21 02:28:01 2010 From: "Rzepa, Henry h.rzepa _ imperial.ac.uk" To: CCL Subject: CCL: AIM Problem Message-Id: <-43430-101221014541-13839-MIEw7ym/++UUcCjG3mnKpQ() server.ccl.net> X-Original-From: "Rzepa, Henry" Content-Type: text/plain; charset="us-ascii" Date: Tue, 21 Dec 2010 06:45:30 +0000 Mime-Version: 1.0 Sent to CCL by: "Rzepa, Henry" [h.rzepa*imperial.ac.uk] >Dear All, > > I am doing AIM analysis of weakly bounded complexes using AIM2000 program.Here, Some of the bond critical points are missing ( like BCP of HCl molecule). What modification should i make in default setting of program? Please help for same. Thanking a lot. > AIM2000 has the option of specifying a starting point. Select the two atomsand iterate. It normally finds it. Or, use AIMALL, which always finds them all. -- +44 (020) 7594 5774 (Voice); Blog: http://www.ch.ic.ac.uk/rzepa/blog/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax). From owner-chemistry@ccl.net Tue Dec 21 03:46:00 2010 From: "may abdelghani may01dz===yahoo.fr" To: CCL Subject: CCL: topological analysis on experimental structure Message-Id: <-43431-101221033725-19996-Uzea3R6gWJ8FYynUGAws5Q^-^server.ccl.net> X-Original-From: may abdelghani Content-Type: multipart/alternative; boundary="0-2050953669-1292920637=:81922" Date: Tue, 21 Dec 2010 08:37:17 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz::yahoo.fr] --0-2050953669-1292920637=:81922 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hello, =0A=0A =0A=0AI have a non negligeble discrepancy=0Abetween the calculated (differe= nt functional and basis sets) and the experimental=0Astructure (0.1 A=B0 in= some bonds). I want to know, if I can=0Aconsidered in my study (a topologi= cal analysis) only the X-ray coordinate. In what extend I have the=0Aright = to perform this methodology? =A0=A0=0A=0A=0A --0-2050953669-1292920637=:81922 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hello,
=0A=0A


=0A=0A

I have a non negl= igeble discrepancy=0Abetween the calculated (different functional an= d basis sets) and the experimental=0Astructure (0.1 A=B0 i= n some bonds). I want to know, if I can=0Aconsidered in my study (a topolog= ical analysis) only the X-ray coordinate. In what extend I have the=0Aright to perform this methodology?   


= =0A=0A=0A=0A=0A --0-2050953669-1292920637=:81922-- From owner-chemistry@ccl.net Tue Dec 21 07:17:00 2010 From: "ehsan shakerzadeh ehsan_shakerzadeh!A!yahoo.com" To: CCL Subject: CCL: Merge a nanotube with other molecule Message-Id: <-43432-101221071517-16317-4skGL+qcXTiWB/6PPj0oCw:_:server.ccl.net> X-Original-From: "ehsan shakerzadeh" Date: Tue, 21 Dec 2010 07:15:16 -0500 Sent to CCL by: "ehsan shakerzadeh" [ehsan_shakerzadeh[*]yahoo.com] Dear all, I want to put a molecule on a nanotube for further studies. First of all I optimized the nanotube and the other structure seperatly. Now I want to put these two structure have an interaaction.with what software I can put them togeter? Is it possible with Gaussview? ehsan shakerzadeh ehsan_shakerzadeh!^!yahoo.com From owner-chemistry@ccl.net Tue Dec 21 08:10:00 2010 From: "ehsan shakerzadeh e-shakerzadeh^scu.ac.ir" To: CCL Subject: CCL: How can merge some structures? Message-Id: <-43433-101221070603-13510-CYzgr1Ti9+9hEWkqGsqkwA,+,server.ccl.net> X-Original-From: "ehsan shakerzadeh" Date: Tue, 21 Dec 2010 07:05:57 -0500 Sent to CCL by: "ehsan shakerzadeh" [e-shakerzadeh,,scu.ac.ir] Dear all, I want to put a molecule on a nanotube for further studies. First of all I optimized the nanotube and the other structure seperatly. Now I want to put these two structure have an interaaction.with what software I can put them togeter? Is it possible with Gaussview? Ehsan Shakerzadeh e-shakerzadeh*scu.ac.ir From owner-chemistry@ccl.net Tue Dec 21 08:51:00 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim..compchem.net" To: CCL Subject: CCL: AIM Problem Message-Id: <-43434-101221084849-1958-Nf7/pSDarmhUDSuEnDy/OQ*o*server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 21 Dec 2010 13:48:41 +0000 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim,,compchem.net] Dear Abhishek I am afraid the BCP of HCl should be detected by AIM2000 using the default setting. Could you let us know how you generated the wfn file? what basis set and method you used? If you like you could send me the wfn on my email for testing it, including the route section used for wfn generation. Merry Christmas M. Ibrahim On Tue, Dec 21, 2010 at 3:51 AM, ABHISHEK SHAHI shahi.abhishek1984^gmail.com wrote: > Dear All, > >    I am doing AIM analysis of weakly bounded complexes using AIM2000 > program.Here, Some of the bond critical points are missing ( like BCP of HCl > molecule). What modification should i make in default setting of program? > Please help for same. Thanking a lot. > > > > > With regards; >  ABHISHEK SHAHI > > Research Scholar > Inorganic and Physical Chemistry > Indian Institute Of Science > Bangalore-12 > > --                   Mahmoud A. A. Ibrahim                        Current Address                  7.05, School of Chemistry,               The 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_+_compchem.net               Website: www.compchem.net                    Fax No.: +20862342601 From owner-chemistry@ccl.net Tue Dec 21 09:25:00 2010 From: "fatemeh moosavi fatemeh.moosavi|*|gmail.com" To: CCL Subject: CCL: Merge a nanotube with other molecule Message-Id: <-43435-101221090519-28636-tceN9kqW1nU1oSzAMbU9sA|server.ccl.net> X-Original-From: fatemeh moosavi Content-Type: multipart/alternative; boundary=001636457ade0a8a7b0497ec2040 Date: Tue, 21 Dec 2010 06:04:52 -0800 MIME-Version: 1.0 Sent to CCL by: fatemeh moosavi [fatemeh.moosavi**gmail.com] --001636457ade0a8a7b0497ec2040 Content-Type: text/plain; charset=ISO-8859-1 Mr Shakerzadeh You can do it by HyperChem software. On Tue, Dec 21, 2010 at 4:15 AM, ehsan shakerzadeh ehsan_shakerzadeh!A! yahoo.com wrote: > > Sent to CCL by: "ehsan shakerzadeh" [ehsan_shakerzadeh[*]yahoo.com] > Dear all, > I want to put a molecule on a nanotube for further studies. > First of all I optimized the nanotube and the other structure seperatly. > Now I want to put these two structure have an interaaction.with what > software I can put them togeter? Is it possible with Gaussview? > ehsan shakerzadeh > ehsan_shakerzadeh\a/yahoo.com> > > --001636457ade0a8a7b0497ec2040 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Mr Shakerzadeh
You can do it by HyperChem software.

On Tue, Dec 21, 2010 at 4:15 AM, ehsan shakerzad= eh ehsan_shakerzadeh!A!yahoo.com <owner-chemistry*ccl= .net> wrote:

Sent to CCL by: "ehsan = =A0shakerzadeh" [ehsan_shakerzadeh[*]yahoo.com]
Dear all,
I want to put a molecule on a nanotube for further studies.First of all I optimized the nanotube and the other structure seperatly. N= ow I want to put these two structure have an interaaction.with what softwar= e I can put them togeter? Is it possible with Gaussview?
ehsan shakerzadeh
ehsan_shakerzadeh\a/yahoo.com



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--001636457ade0a8a7b0497ec2040-- From owner-chemistry@ccl.net Tue Dec 21 10:00:00 2010 From: "Jacco van de Streek vandestreek-x-avmatsim.de" To: CCL Subject: CCL: topological analysis on experimental structure Message-Id: <-43436-101221093138-3590-WzPAl+q2ObipMAJqZsUfWA]~[server.ccl.net> X-Original-From: Jacco van de Streek Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 21 Dec 2010 15:31:03 +0100 MIME-Version: 1.0 Sent to CCL by: Jacco van de Streek [vandestreek ~ avmatsim.de] On 12/21/2010 09:37 AM, may abdelghani may01dz===yahoo.fr wrote: > I have a non negligeble discrepancy between the calculated (different > functional and basis sets) and the experimental structure(0.1 A° in some > bonds). I want to know, if I can considered in my study (a topological > analysis) only the X-ray coordinate. In what extend I have the > righttoperform this methodology? Bond lengths in crystal structures can easily be off by 0.1 A from the correct value in certain cases. What are the two elements of these bonds, e.g. are they C-C bonds or C-H bonds? Do you have the original data including the anisotropic displacement parameters or do you only have the atomic coordinates? Best wishes, -- Dr Jacco van de Streek Senior Scientist Avant-garde Materials Simulation Freiburg im Breisgau, Germany From owner-chemistry@ccl.net Tue Dec 21 12:02:00 2010 From: "may abdelghani may01dz\a/yahoo.fr" To: CCL Subject: CCL: Re : CCL: topological analysis on experimental structure Message-Id: <-43437-101221115411-4749-Oxw5q+gKHMRQAr74wEUh2g#,#server.ccl.net> X-Original-From: may abdelghani Content-Type: multipart/alternative; boundary="0-1259173860-1292950443=:99497" Date: Tue, 21 Dec 2010 16:54:03 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz(a)yahoo.fr] --0-1259173860-1292950443=:99497 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable =0A=0Asir,=20 1. What=0Aare the two elements of these bonds e.g. are they C-C bonds or C-= H bonds? I have 2 types of bonds (experimental /calculate): C-C(1.88=0A A=B0/1.2= 8A=B0) =A0and Ru-C (2.346A=B0/2.590;=0A 2.138 A=B0/2.044A=B0) bonds. =0A=0A=0A=0A2.Do=0Ayou have the original data including the anisotropic dis= placement parameters or=0Ado you only have the atomic coordinates? =0A=0Aunfortunately =A0I have =A0only the atomic coordinates=20 --- En date de=A0: Mar 21.12.10, Jacco van de Streek vandestreek-x-avmatsim= .de a =E9crit=A0: De: Jacco van de Streek vandestreek-x-avmatsim.de Objet: CCL: topological analysis on experimental structure =C0: "Abdelghani, May " Date: Mardi 21 d=E9cembre 2010, 15h31 Sent to CCL by: Jacco van de Streek [vandestreek ~ avmatsim.de] On 12/21/2010 09:37 AM, may abdelghani may01dz=3D=3D=3Dyahoo.fr wrote: > I have a non negligeble discrepancy between the calculated (different > functional and basis sets) and the experimental structure(0.1 A=B0 in som= e > bonds). I want to know, if I can considered in my study (a topological > analysis) only the X-ray coordinate. In what extend I have the > righttoperform this methodology?=A0=20 Bond lengths in crystal structures can easily be off by 0.1 A from the correct value in certain cases. What are the two elements of these bonds, e.g. are they C-C bonds or C-H bonds? Do you have the original data including the anisotropic displacement parameters or do you only have the atomic coordinates? Best wishes, --=20 Dr Jacco van de Streek Senior Scientist Avant-garde Materials Simulation Freiburg im Breisgau, Germany -=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 --0-1259173860-1292950443=:99497 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
=0A=0A<= p class=3D"MsoNormal" style=3D"text-align: left; direction: ltr; unicode-bi= di: embed;">sir,

1. What=0Aare the two elements of the= se bonds e.g. are they C-C bonds or C-H bonds?


I have 2 types of bonds (experimental /calculate): C-C(1.88=0A A=B0/1= .28A=B0)  and Ru-C (2.346A=B0/2.590;=0A 2.= 138 A=B0/2.044A=B0) bonds.


=0A=0A=0A=0A

2.Do=0Ayou have the original data including the anisotropic displac= ement parameters or=0Ado you only have the atomic coordinates?


=0A=0A

<= /span>unfortunately  I have  only the atomic coordinates



--- En date de : Mar 21.12.10, Jacco van de Str= eek vandestreek-x-avmatsim.de <owner-chemistry*|*ccl.net> a = =E9crit :

De: Jacco van de Streek vand= estreek-x-avmatsim.de <owner-chemistry*|*ccl.net>
Objet: CCL: topolo= gical analysis on experimental structure
=C0: "Abdelghani, May "= <may01dz*|*yahoo.fr>
Date: Mardi 21 d=E9cembre 2010, 15h31


Sent to CCL by: Jacco van de Str= eek [vandestreek ~ avmatsim.de]
On 12/21/2010 09:37 AM, may abdelghani m= ay01dz=3D=3D=3Dyahoo.fr wrote:
> I have a non negligeble discrepancy = between the calculated (different
> functional and basis sets) and th= e experimental structure(0.1 A=B0 in some
> bonds). I want to know, i= f I can considered in my study (a topological
> analysis) only the X-= ray coordinate. In what extend I have the
> righttoperform this metho= dology? 

Bond lengths in crystal structures can easily be off = by 0.1 A from the
correct value in certain cases. What are the two eleme= nts of these
bonds, e.g. are they C-C bonds or C-H bonds? Do you have th= e original
data including the anisotropic displacement parameters or do = you only
have the atomic coordinates?

Best wishes,
--
Dr J= acco van de Streek
Senior Scientist
Avant-garde Materials Simulation
Freiburg im Breisgau, Germany



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=0A=0A=0A=0A=0A --0-1259173860-1292950443=:99497-- From owner-chemistry@ccl.net Tue Dec 21 15:52:00 2010 From: "Eliac Brown Eliacbrown(!)yahoo.com" To: CCL Subject: CCL:G: G09 error Message-Id: <-43438-101221155116-5847-0BKa6iwLrIZUdI9fbSMW0A|server.ccl.net> X-Original-From: "Eliac Brown" Date: Tue, 21 Dec 2010 15:51:15 -0500 Sent to CCL by: "Eliac Brown" [Eliacbrown_._yahoo.com] Dear CCL In G09, running pop=mk using "any" semi empirical method job ends with this error: Missing nuc terms in AM1 ESP do you how I can solve this error? The job terminates normally in G03 merry xmas Eliac