From owner-chemistry@ccl.net Mon Dec 7 09:09:01 2009 From: "Peter Maas peter.maas|,|specs.net" To: CCL Subject: CCL: 3D to 2D conversion Message-Id: <-40873-091204115130-9941-FTXi51Bp2IOE0vnDhT/gXA*_*server.ccl.net> X-Original-From: "Peter Maas" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 4 Dec 2009 16:51:08 +0100 MIME-Version: 1.0 Sent to CCL by: "Peter Maas" [peter.maas..specs.net] Dear Andrey, If you use the SD-file table editor from Bioclipse all structures will be displayed in 2D on the fly. It handles real big SD-files (I opened 300,000 2D structures with it) and still is pretty fast. You can download it from http://www.bioclipse.net/ Good luck, Peter ------------------------------------------------------ Specs Kluyverweg 6 2629 HT DELFT The Netherlands p +31 15 2518111 (office) p +31 15 2518139 (direct) f +31 15 2518181 peter.maas#specs.net www.specs.net ------------------------------------------------------ > -----Original Message----- > From: owner-chemistry+peter.maas==specs.net#ccl.net [mailto:owner- > chemistry+peter.maas==specs.net#ccl.net] On Behalf Of Andrey E Voronkov > drugdesign##yandex.ru > Sent: Tuesday, 01 December, 2009 12:10 > To: Maas, Peter > Subject: CCL: 3D to 2D conversion > > > Sent to CCL by: "Andrey E Voronkov" [drugdesign~~yandex.ru] > Dear CCL users, > wouldn't you be so kind to recommend the software for 3D to 2D conversion for > chemical databases. The problem is that I have the results of virtuial > screening in 3D SDF format which I want todisplay as planar, just visualize as > organic molecule structures datasets. Are there any viewers which uatomatically > covert 3D to 2D? > > Best regards, > Andrew From owner-chemistry@ccl.net Mon Dec 7 09:44:00 2009 From: "Joaquin Barroso Flores joaco_barroso%a%yahoo.com" To: CCL Subject: CCL:G: how to build a polythiophene unit cell for a pbc gaussian calculation Message-Id: <-40874-091207051011-5119-WEUMkgfr0WoauN1Dz7XwLw . server.ccl.net> X-Original-From: Joaquin Barroso Flores Content-Type: multipart/alternative; boundary="0-652871099-1260180597=:26747" Date: Mon, 7 Dec 2009 02:09:57 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Joaquin Barroso Flores [joaco_barroso]~[yahoo.com] --0-652871099-1260180597=:26747 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi Daniel=0A=0ARemember me? I went to Chihuahua a couple of times with the = CIP team. OK about your question. You can do this also if you have Gaussvie= w in the following way:=0ABuild your repeating unit of thiophene in terms o= f an assymetric unit (I'm assuming two would be fine to get one S atom poin= ting in one direction and another pointing in the opposite one). Delete one= Hydrogen atom in alpha positions to an S atom and replace the other one (t= he symmetry related one) with a carbon atom.=0AThen go to EDIT -> PBC This = will open a dialog window. =0AOn the first tab (Symmetry) select Lattice Di= mensions =3D1 (you may activate line group symmetry and constraints)=0AOn = the second tab (Cell) click on the button "Place" This will allow you to mo= ve and define your translation vector Tv (make sure Location has the option= "Atom" selected) There you see Vertex: O(0) Click on the Dummy atom and th= is should place the origin of the Tv on it. Then change Vertex to a(1) and = click on the "naked C" atom at the other end of the molecule, this will now= place the end of the vector at it.=0AOn the third tab (View) you may now r= eplicate the cell backwards and forwards by increasing the number in both t= he a and -a directions, respectively.=0AOn the fourth tab (contents) delete= the extra C atom you placed on step one.=0A=0ACheck also the Gaussview hel= p at gaussian.com. It should be located under tech support. =0A=0AI hope th= is helps!=0A=0APlease say hi to your group=0A=0AJoaquin=0A=0A =3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=0AJoa= quin Barroso-Flores, Ph. D.=0AFacultatea de Chimie, Universitatea Babes-Bol= yai=0ACluj-Napoca, Romania=0A=0A=0A-> http://joaquinbarroso.com=0A-> http:/= /joaquinbarroso.wordpress.com=0A=0A=0Ajoaquinbarroso''a''chem.ubbcluj.ro=0A= joaquin.barroso''a''gmail.com =0A=0A=0A"Blogastronom=EDa": http://joaquinba= rroso.blogspot.com =0A=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=0A=0A=0A=0A=0A______________________________= __=0ADe: Daniel Glossman-Mitnik dglossman+*+gmail.com =0APara: "Flores, Joaquin Barroso " = =0AEnviado: s=E1bado, 5 de diciembre, 2009 2:48:49=0AAsunto: CCL:G: how to = build a polythiophene unit cell for a pbc gaussian calculation=0A=0A=0ADear= netters:=0A=0AI will be pleased if you can point me to a (step by step) gu= ide on how to build a polythiophene =0Aunit cell for a pbc gaussian calcula= tion, using GaussView or any other program.=0APlease note: I don=B4t need o= nly the input file, I want to learn how to build the unit cell.=0A=0AThanks= in advance,=0A=0ADaniel=0A=0A*********************************************= ******************************************************************=0ADr. Da= niel Glossman-Mitnik:=0ACentro de Investigaci=F3n en Materiales Avanzados, = SC=0AGrupo NANOCOSMOS - Modelado Molecular y Simulaci=F3n Computacional d= e Nanomateriales=0AMiguel de Cervantes 120 - Complejo Industrial Chihuahua = - Chihuahua, Chih 31109, Mexico=0APhone: +52 614 4391151 Secretary/FAX:= +52 614 4394852 Lab: +52 614 4394805=0AE-mail: daniel.glossman++cimav= .edu.mx dglossman++gmail.com=0AWWW: http://www.cimav.edu.mx/cv/da= niel.glossman=0A http://blogs.cimav.edu.mx/daniel.glossman=0A**= ***************************************************************************= **********************************=0A=0A=0A=0A Encuentra las mejores r= ecetas en Yahoo! Cocina. =0Ahttp://mx.mujer.yahoo.com= /cocina/ --0-652871099-1260180597=:26747 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Daniel

Remember me? I went to Chihuahua a couple of = times with the CIP team. OK about your question. You can do this also if yo= u have Gaussview in the following way:
Build your repeating unit of thio= phene in terms of an assymetric unit (I'm assuming two would be fine to get= one S atom pointing in one direction and another pointing in the opposite = one). Delete one Hydrogen atom in alpha positions to an S atom and replace = the other one (the symmetry related one) with a carbon atom.
Then go to = EDIT -> PBC This will open a dialog window.
On the first tab (Symmet= ry) select Lattice Dimensions =3D1 (you  may activate line group symme= try and constraints)
On the second tab (Cell) click on the button "Place= " This will allow you to move and define your translation vector Tv (make sure Location has the option "Atom" selected) There you see Vertex: O(0) C= lick on the Dummy atom and this should place the origin of the Tv on it. Th= en change Vertex to a(1) and click on the "naked C" atom at the other end o= f the molecule, this will now place the end of the vector at it.
On the = third tab (View) you may now replicate the cell backwards and forwards by i= ncreasing the number in both the a and -a directions, respectively.
On t= he fourth tab (contents) delete the extra C atom you placed on step one.
Check also the Gaussview help at gaussian.com. It should be located un= der tech support.

I hope this helps!

Please say hi to your g= roup

Joaquin
 
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Joaquin Barroso-Flores,= Ph. D.
Facultatea de Chimie, Universitatea Babes-Bolyai
Cluj-Napoca,= Romania



joaqu= inbarroso''a''chem.ubbcluj.ro
joaquin.barroso''a''gmail.com

"Blogastronom=EDa": http://joaquinbarroso.blogspot.com
= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D


<= hr size=3D"1">De: Daniel G= lossman-Mitnik dglossman+*+gmail.com <owner-chemistry*_*ccl.net>
= Para: "Flores, Joaquin Barros= o " <joaco_barroso*_*yahoo.com>
E= nviado: s=E1bado, 5 de diciembre, 2009 2:48:49
Asunto: CCL:G: how to build a polythioph= ene unit cell for a pbc gaussian calculation


Dear netters= :

I will be pleased if you can point me to a (step by step) guide on= how to build a polythiophene
unit cell for a pbc gaussian calculation,= using GaussView or any other program.
Please note: I don=B4t need only = the input file, I want to learn how to build the unit cell.
=0A
Thank= s in advance,

Daniel

**************************= ***************************************************************************= **********
Dr. Daniel Glossman-Mitnik:
Centro de Investigaci=F3n en M= ateriales Avanzados, SC
=0AGrupo NANOCOSMOS  -  Modelado Molec= ular y Simulaci=F3n Computacional de Nanomateriales
Miguel de Cervantes = 120 - Complejo Industrial Chihuahua - Chihuahua, Chih 31109, Mexico
Phon= e: +52 614 4391151     Secretary/FAX: +52 614 4394852   &nbs= p; Lab: +52 614 4394805
=0AE-mail:  daniel.glossman++cimav.edu.mx     =      dglossman++gmai= l.com
WWW:  http://www.cimav.edu.mx/cv/daniel.gl= ossman
=0A              http://blogs.cimav.edu.mx/daniel.glossman
*********************= ***************************************************************************= ***************
=0A=0A
=0A=0A

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

=A1Encuentra las mejo= res recetas
con Yahoo! Cocina!
=0Ahttp://mx.mujer.yahoo.com/cocina/ --0-652871099-1260180597=:26747-- From owner-chemistry@ccl.net Mon Dec 7 10:19:00 2009 From: "Nicolas Staelens nicolas.staelens_-_fundp.ac.be" To: CCL Subject: CCL: TINKER MM2.prm Sulfur Params Message-Id: <-40875-091207091424-15600-ofJpuvyGrxbJnMT9VgMt2A~!~server.ccl.net> X-Original-From: Nicolas Staelens Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes Date: Mon, 7 Dec 2009 14:41:20 +0100 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Nicolas Staelens [nicolas.staelens:fundp.ac.be] The two first numbers are the atom types, 3.213 is the force constant =20= (in the Hooke-like bond stretching term) and 1.815 is the equilibrium =20= length of the bond (in =C5). You will also have to add the Angle Bending Parameters, Stretch-Bend =20 Parameters, and the Torsional Parameters related to that sequence of =20 atoms. Have a nice day Nicolas Staelens Ph D Student University of Namur, Belgium Le 5 Dec 2009 =E0 16:49, Ryan Kopreski rpkopreski]_[gmail.com a =E9crit = : > > Sent to CCL by: "Ryan Kopreski" [rpkopreski(!)gmail.com] > I am a new user of the TINKER package and would like to optimize a =20 > structure containing a Csp2-S-Csp3 moiety using the mm2 parameter =20 > set, but I get an error due to missing parameters for the atoms =20 > about sulfur. > > I do not understand some of the columns in the mm2.prm file, but =20 > thought I might be able to add the missing params from data I have =20 > obtained optimizing similar structures with Chem3D. Could someone =20 > help me understand this file? Or better, does anyone have a modified =20= > mm2.prm file for this C-S-C atom set? > > Example interpretation from mm2.prm: > > atom types ? bond length (A) > bond 1 15 3.213 1.815 > > As you can see, I do not know what is the meaning of column 4 in the =20= > "bond" parameter list, and I have not found any information from the =20= > web on this yet. > > I appreciate any clues/suggestions/assistance! > > Ryan Kopreski > rpkopreski(at)gmail(dot)com > > > > -=3D This is automatically added to each message by the mailing script = =20 > =3D- > To recover the email address of the author of the message, please =20 > change> Conferences: http://server.ccl.net/chemistry/announcements/=20 > conferences/>