From owner-chemistry@ccl.net Wed Jun 2 09:22:00 2010 From: "Morad El-Hendawy m80elhendawy ~~ yahoo.com" To: CCL Subject: CCL:G: To perform constrained Optimization. Message-Id: <-42040-100602083255-30776-OPYBOhNxxiooABKVUCTQww===server.ccl.net> X-Original-From: Morad El-Hendawy Content-Type: multipart/alternative; boundary="0-2004368471-1275478365=:20098" Date: Wed, 2 Jun 2010 04:32:45 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Morad El-Hendawy [m80elhendawy[-]yahoo.com] --0-2004368471-1275478365=:20098 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Santhanamoorthi, A good way to=A0 fix=A0 two unbonded atoms at a particular distance during = the optimization is doing partial optimization using opt=3Dz-matrix. Genera= te the coordinates of your molecule as Z-matrix and then as Cartesian coord= inates. Copy XYZ values for both atoms then past in their corresponding pos= itions in Z-matrix i.e. mixed coordinates. By this method you gave constant= values for the positions of these atoms during the optimization. Opt=3Dz-m= atrix is necessary for such input file. Cheers, Morad=20 --- On Tue, 6/1/10, santhanamoorthi N santhanamoorthi[#]rediffmail.com wrote: > From: santhanamoorthi N santhanamoorthi[#]rediffmail.com Subject: CCL:G: To perform constrained Optimization. To: "El-Hendawy, Morad Metwally " Date: Tuesday, June 1, 2010, 12:03 PM Sent to CCL by: "santhanamoorthi=A0 N" [santhanamoorthi]-[rediffmail.com] Is it Possible to fix the two unbonded atoms at a particular distance while= optimization? For example, in Dipeptide, i want to fix the Two oxygen atom= s at a particular distance. Is it possible in Gaussian?=20 Thanks in Advance -=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 --0-2004368471-1275478365=:20098 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Santhanamoorthi,
A good way to  = fix  two unbonded atoms at a particular distance during the optimizati= on is doing partial optimization using opt=3Dz-matrix. Generate the coordin= ates of your molecule as Z-matrix and then as Cartesian coordinates. Copy XYZ values for both atoms then pas= t in their corresponding positions in Z-matrix i.e. mixed coordinates. By t= his method you gave constant values for the positions of these atoms during= the optimization. Opt=3Dz-matrix is necessary for such input file.
Chee= rs,
Morad

--- On Tue, 6/1/10, santhanamoorthi N santhanamoort= hi[#]rediffmail.com <owner-chemistry~!~ccl.net> wrote:

From: santhanamoorthi N santhanamoorthi[#]rediff= mail.com <owner-chemistry~!~ccl.net>
Subject: CCL:G: To perform constrained = Optimization.
To: "El-Hendawy, Morad Metwally " <m80elhendawy= ~!~yahoo.com>
Date: Tuesday, June 1, 2010, 12:03 PM


Sent to CCL by: "santhanamoorthi  N" [santhanamoort= hi]-[rediffmail.com]
Is it Possible to fix the two unbonded atoms at a p= articular distance while optimization? For example, in Dipeptide, i want to= fix the Two oxygen atoms at a particular distance. Is it possible in Gauss= ian?

Thanks in Advance



-=3D This is automatically ad= ded to each message by the mailing script =3D-
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=0A=0A=0A=0A=0A=0A=0A=0A --0-2004368471-1275478365=:20098-- From owner-chemistry@ccl.net Wed Jun 2 14:17:00 2010 From: "Esteban Gabriel Vega Hissi egvega:-:gmail.com" To: CCL Subject: CCL:G: To perform constrained Optimization. Message-Id: <-42041-100602122421-28559-i8B95ybVcWd4sX7+ogk/5w{=}server.ccl.net> X-Original-From: Esteban Gabriel Vega Hissi Content-Type: multipart/alternative; boundary=0016363b9e701ec1b604880cf56a Date: Wed, 2 Jun 2010 16:32:00 +0200 MIME-Version: 1.0 Sent to CCL by: Esteban Gabriel Vega Hissi [egvega .. gmail.com] --0016363b9e701ec1b604880cf56a Content-Type: text/plain; charset=ISO-8859-1 Hi Morad, If you do so, fixing xyz positions of 2 atoms your don't let them move at all, so there will be other variables involving other atoms that won't optimize , and what you want to fix is only the distance between them. I insist that reduntant coordinates can be used. Esteban G. Vega Hissi UNSL -- On Wed, Jun 2, 2010 at 1:32 PM, Morad El-Hendawy m80elhendawy ~~ yahoo.com < owner-chemistry[A]ccl.net> wrote: > Dear Santhanamoorthi, > A good way to fix two unbonded atoms at a particular distance during the > optimization is doing partial optimization using opt=z-matrix. Generate the > coordinates of your molecule as Z-matrix and then as Cartesian coordinates. > Copy XYZ values for both atoms then past in their corresponding positions > in Z-matrix i.e. mixed coordinates. By this method you gave constant values > for the positions of these atoms during the optimization. Opt=z-matrix is > necessary for such input file. > Cheers, > Morad > > --- On *Tue, 6/1/10, santhanamoorthi N santhanamoorthi[#]rediffmail.com < > owner-chemistry-x-ccl.net>* wrote: > > > From: santhanamoorthi N santhanamoorthi[#]rediffmail.com < > owner-chemistry-x-ccl.net> > Subject: CCL:G: To perform constrained Optimization. > To: "El-Hendawy, Morad Metwally " > Date: Tuesday, June 1, 2010, 12:03 PM > > > Sent to CCL by: "santhanamoorthi N" [santhanamoorthi]-[rediffmail.com] > Is it Possible to fix the two unbonded atoms at a particular distance while > optimization? For example, in Dipeptide, i want to fix the Two oxygen atoms > at a particular distance. Is it possible in Gaussian? > > Thanks in Advance> the strange characters on the top line to the -x- sign. You can also> > E-mail to subscribers: CHEMISTRY-x-ccl.netor use:> > E-mail to administrators: CHEMISTRY-REQUEST-x-ccl.netor use> > > > --0016363b9e701ec1b604880cf56a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Morad,

If you do so, fixing xyz positions of 2 atoms your don'= ;t let them move at all, so there will be other variables involving other a= toms that won't optimize , and what you want to fix is only the distanc= e between them.
I insist that reduntant coordinates can be used.

Esteban G. Vega His= si
UNSL

--
On Wed, Jun 2, 2010 at 1= :32 PM, Morad El-Hendawy m80elhendawy ~~ yahoo= .com <o= wner-chemistry[A]ccl.net> wrote:
Dear Santhanamoorthi,
A good way to=A0 fix=A0 two unbonded atoms at a pa= rticular distance during the optimization is doing partial optimization usi= ng opt=3Dz-matrix. Generate the coordinates of your molecule as Z-matrix an= d then as Cartesian coordinates. Copy XY= Z values for both atoms then past in their corresponding positions i= n Z-matrix i.e. mixed coordinates. By this method you gave constant values = for the positions of these atoms during the optimization. Opt=3Dz-matrix is= necessary for such input file.
Cheers,
Morad

--- On Tue, 6/1/10, santhanamoorthi N santhanam= oorthi[#]rediffmail.com= <= owner-chemistry-x-ccl.net> wrote:

From: santhanamoorthi N santhanamoorthi[#]rediffmail.com <owner-c= hemistry-x-ccl.net>
Subject: CCL:G: To perform constrained Optimi= zation.
To: "El-Hendawy, Morad Metwally " <m80elhendawy-x-yahoo.com&= gt;
Date: Tuesday, June 1, 2010, 12:03 PM


Sent to CCL by: "= ;santhanamoorthi=A0 N" [santhanamoorthi]-[rediffmail.com]
Is it Possible to fix the tw= o unbonded atoms at a particular distance while optimization? For example, = in Dipeptide, i want to fix the Two oxygen atoms at a particular distance. = Is it possible in Gaussian?

Thanks in Advance



-=3D This is automatically added to ea= ch message by the mailing script =3D-
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--0016363b9e701ec1b604880cf56a-- From owner-chemistry@ccl.net Wed Jun 2 14:51:01 2010 From: "Christoph Steinbeck steinbeck~~ebi.ac.uk" To: CCL Subject: CCL: ChEBI user workshop, 23rd and 24th June 2010, Hinxton, Cambridge, UK Message-Id: <-42042-100602113759-20162-5evXSggXnibZB+3WyvNp+Q~!~server.ccl.net> X-Original-From: Christoph Steinbeck Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252 Date: Wed, 02 Jun 2010 15:23:22 +0100 MIME-Version: 1.0 Sent to CCL by: Christoph Steinbeck [steinbeck . ebi.ac.uk] ChEBI (Chemical Entities of Biological Interest) is the Chemistry Database and Chemical Ontology of the European Bioinformatics Institute (EBI) in Hinxton, Cambridge, UK. We are pleased to invite you to attend our second ChEBI User Group Workshop, which will take place in the IT Training Room at the European Bioninformatics Institute in on the 23rd and 24th June 2010. There will be an exciting line-up of speakers, including Peter Ertl from Novartis speaking about his cheminformatics analysis of Natural Products Space, and several intensive discussion sessions during which you will be given the opportunity to influence the future evolution of the ChEBI project. We will also provide training on ChEBI including using ChEBI for research purposes and submitting your chemicals to ChEBI for annotation. Information about the workshop, including the full provisional schedule and the link for registration, is available at www.ebi.ac.uk/training/onsite/CHEBI_230610.html. We hope to welcome you to Hinxton in June. Kind regards, the ChEBI team. -- Dr. Christoph Steinbeck Head of Chemoinformatics and Metabolism European Bioinformatics Institute (EBI) Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD UK Phone +44 1223 49 2640; Mobile +44 7826 522319 Video meliora proboque deteriora sequor. ... Ovid, Metamorphoses VII, 20/21 From owner-chemistry@ccl.net Wed Jun 2 15:26:01 2010 From: "Morad El-Hendawy m80elhendawy*yahoo.com" To: CCL Subject: CCL:G: To perform constrained Optimization. Message-Id: <-42043-100602145957-3477-wtWlVHk+9omoiCTBm+CnrA%server.ccl.net> X-Original-From: Morad El-Hendawy Content-Type: multipart/alternative; boundary="0-247625120-1275505186=:28329" Date: Wed, 2 Jun 2010 11:59:46 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Morad El-Hendawy [m80elhendawy a yahoo.com] --0-247625120-1275505186=:28329 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Esteban, It depends on the purpose of Santhanamoorthi. The way I suggested will fix = both the positions and the distance between two atoms. While=A0 using redun= tant coordinates will fix the distance only. The later can be done by more = than one techniques. The former way is important often when=A0 an electric = field is applied on the protein.=20 My regards, Morad --- On Wed, 6/2/10, Esteban Gabriel Vega Hissi egvega:-:gmail.com wrote: > From: Esteban Gabriel Vega Hissi egvega:-:gmail.com Subject: CCL:G: To perform constrained Optimization. To: "El-Hendawy, Morad Metwally " Date: Wednesday, June 2, 2010, 5:32 PM Hi Morad, If you do so, fixing xyz positions of 2 atoms your don't let them move at a= ll, so there will be other variables involving other atoms that won't optim= ize , and what you want to fix is only the distance between them. =0A=0AI insist that reduntant coordinates can be used. Esteban G. Vega Hissi UNSL -- On Wed, Jun 2, 2010 at 1:32 PM, Morad El-Hendawy m80elhendawy ~~ yahoo.com = wrote: =0A=0A=0A=0ADear Santhanamoorthi, A good way to=A0 fix=A0 two unbonded atoms at a particular distance during = the optimization is doing partial optimization using opt=3Dz-matrix. Genera= te the coordinates of your molecule as Z-matrix and then as Cartesian coord= inates. Copy XYZ values for both atoms then past in their corresponding pos= itions in Z-matrix i.e. mixed coordinates. By this method you gave constant= values for the positions of these atoms during the optimization. Opt=3Dz-m= atrix is necessary for such input file. =0A=0ACheers, Morad=20 --- On Tue, 6/1/10, santhanamoorthi N santhanamoorthi[#]rediffmail.com wrote: =0A=0A > From: santhanamoorthi N santhanamoorthi[#]rediffmail.com=0A Subject: CCL:G: To perform constrained Optimization. To: "El-Hendawy, Morad Metwally " =0A=0ADate: Tuesday, June 1, 2010, 12:03 PM Sent to CCL by: "santhanamoorthi=A0 N" [santhanamoorthi]-[rediffmail.com] Is it Possible to fix the two unbonded atoms at a particular distance while= optimization? For example, in Dipeptide, i want to fix the Two oxygen atom= s at a particular distance. Is it possible in Gaussian?=20 =0A=0A Thanks in Advance -=3D This is automatically added to each message by the mailing script =3D-the strange characters on the top line to the -x- sign. You can also E-mail to subscribers: CHEMISTRY-x-ccl.net or use: =A0 =A0 =A0=0A=0A E-mail to administrators: CHEMISTRY-REQUEST-x-ccl.net or use =A0 =A0 =A0=0A=0A=A0 =A0 =A0=0A=0A Job: http://www.ccl.net/jobs=20=0A=0A=A0 =A0 =A0=0A=0A=0A=0A=0A=0A=0A=0A=0A=0A =20 =0A=0A=0A=0A --0-247625120-1275505186=:28329 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Esteban,
It depends on the purpose of= Santhanamoorthi. The way I suggested will fix both the positions and the d= istance between two atoms. While  using reduntant coordinates will fix= the distance only. The later can be done by more than one techniques. The = former way is important often when  an electric field is applied on th= e protein.
My regards,
Morad


--- On Wed, 6/2/10, Esteb= an Gabriel Vega Hissi egvega:-:gmail.com <owner-chemistry,+,ccl.net>= wrote:

From: Esteban Gabriel Vega = Hissi egvega:-:gmail.com <owner-chemistry,+,ccl.net>
Subject: CCL:G:= To perform constrained Optimization.
To: "El-Hendawy, Morad Metwally -i= d#3wg-" <m80elhendawy,+,yahoo.com>
Date: Wednesday, June 2, 2010, 5:= 32 PM

Hi Morad,

If you do so, fixing x= yz positions of 2 atoms your don't let them move at all, so there will be o= ther variables involving other atoms that won't optimize , and what you wan= t to fix is only the distance between them.
=0A=0AI insist that reduntan= t coordinates can be used.

Esteban G. Vega Hissi
UNSL

--
On Wed, Jun 2, 2010 at 1:32 PM, Morad El-Henda= wy m80elhendawy ~~ yahoo.com <owner-chemistry**ccl.net> wrote:=
=0A=0A
=0A=0ADear Santhanamoorthi,
= A good way to  fix  two unbonded atoms at a particular distance d= uring the optimization is doing partial optimization using opt=3Dz-matrix. = Generate the coordinates of your molecule as Z-matrix and then as Cartesian= coordinates. Copy XYZ values for= both atoms then past in their corresponding positions in Z-matrix i.e. mix= ed coordinates. By this method you gave constant values for the positions o= f these atoms during the optimization. Opt=3Dz-matrix is necessary for such= input file.
=0A=0ACheers,
Morad

--- On Tue, 6/1/10, santh= anamoorthi N santhanamoorthi[#]rediffmail.com <owner-chemistry-x= -ccl.net> wrote:
=0A=0A

From:= santhanamoorthi N santhanamoorthi[#]rediffmail.com=0A <owner-chemist= ry-x-ccl.net>
Subject: CCL:G: To perform constrained Optimization= .
To: "El-Hendawy, Morad Metwally " <m80elhendawy-x-yahoo.com= >
=0A=0ADate: Tuesday, June 1, 2010, 12:03 PM


Sent to= CCL by: "santhanamoorthi  N" [santhanamoorthi]-[rediffmail.com]
Is i= t Possible to fix the two unbonded atoms at a particular distance while opt= imization? For example, in Dipeptide, i want to fix the Two oxygen atoms at= a particular distance. Is it possible in Gaussian?
=0A=0A
Thanks in= Advance



-=3D This is automatically added to each message by= the mailing script =3D-
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the strange characters on the top line to the = -x- sign. You can also

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=
=0A=0A --0-247625120-1275505186=:28329-- From owner-chemistry@ccl.net Wed Jun 2 16:01:00 2010 From: "Roger Robinson scu98rkr##gmail.com" To: CCL Subject: CCL: Internal Rotation Symmetry numbers Message-Id: <-42044-100602145406-30878-wfj7sD7Fi0lDGmsq44M44g+*+server.ccl.net> X-Original-From: Roger Robinson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 02 Jun 2010 18:55:29 +0100 MIME-Version: 1.0 Sent to CCL by: Roger Robinson [scu98rkr,,gmail.com] Hi, If an Internal Rotation has 3 energy Minimum and Maximum as the bond is rotated. That rotation has a symmetry of 3. The energy as the bond when rotated will look something like this /\/\/\ Again if there were 2 Minimum and Maximum the symmetry number is 2. /\/\ But what if there 2 Maximums same but just 1 Minimum ? or alternative 1 Maximum but 2 Minima. The graph of the scan still has a symmetry of 2 but what is the symmetry number of the rotation. At the 2 maxima the geometries are the indistinguishable but not at the mimina. ie C=CC=C. The graph would look something like this where the central minima is somewhat different from the other minima. /\_/\ Cheers