From owner-chemistry@ccl.net Sat Jun 7 10:22:00 2014 From: "John Keller jwkeller%%alaska.edu" To: CCL Subject: CCL: Looking for a conformer generator program Message-Id: <-50183-140607003830-29760-/dTV3o2+EyubDzykNYkCzw%x%server.ccl.net> X-Original-From: John Keller Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Fri, 6 Jun 2014 20:38:20 -0800 Mime-Version: 1.0 (1.0) Sent to CCL by: John Keller [jwkeller__alaska.edu] Gustavo, Hyperchem has a 10 day evaluation period. It has a very nice automated conformation search using the directed Monte Carlo method of W. Clark Still. John Keller University of Alaska Fairbanks > On Jun 5, 2014, at 5:59 PM, "Gustavo L.C. Moura gustavo.moura*_*ufpe.br" wrote: > > > Sent to CCL by: "Gustavo L.C. Moura" [gustavo.moura=ufpe.br] > Dear CCL community, > I have been searching for a conformer generator program that can handle acyclic compounds (none of my molecules have flexible rings, yet). I have already tested a few programs, and so far, none has worked to my satisfaction. The program I am looking for should obey some requirements. The requirements are: > 1) The program should use the RMSD of the coordinates to check for equivalent conformers. The first program that I tested employed only the energy to differentiate conformers and was unable to differentiate non-superimposable conformers that happen to have the same energy. > 2) I am not overly concerned with the quality of the molecular mechanics forcefield that will be employed by the program to optimize the geometries of the conformers because I will reoptimize them with quantum chemical methods. However, I need to have a forcefield that is able to handle selenium atoms. > 3) The program should be capable of generating conformers resulting from the rotation around C-OH and C-NH2 bonds. My interest is in the spectroscopic properties (UV-VIS and NMR) of my molecules and rotations around such bonds are very important to me. > So, does anyone on the list know of a conformer generator program that has the characteristics above? > Thank you very much in advance. > Sincerely yours, > Gustavo L.C. Moura> > From owner-chemistry@ccl.net Sat Jun 7 11:18:01 2014 From: "Marchese, Prof. Francis T. fmarchese/./pace.edu" To: CCL Subject: CCL: Movie Recommendation Message-Id: <-50184-140607110202-25632-bxN0iylOVhLV9wH9tWVGfg-.-server.ccl.net> X-Original-From: "Marchese, Prof. Francis T." Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_7E2BCCBD9F13D747B02B65E69417735C482204C6exchnycmbx01pac_" Date: Sat, 7 Jun 2014 15:01:45 +0000 MIME-Version: 1.0 Sent to CCL by: "Marchese, Prof. Francis T." [fmarchese^^^pace.edu] --_000_7E2BCCBD9F13D747B02B65E69417735C482204C6exchnycmbx01pac_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable All, This movie recommendation may arrive a bit late, but there is one more show= ing (Sunday at 9PM) of a recent Italian comedy "I Can Quit Whenever I Want = (Smetto Quando Voglio) at the Walter Reade Theater in Lincoln Center (new Y= ork City). See link: http://www.filmlinc.com/films/on-sale/i-can-quit-whene= ver-i-want. It is about a computational chemist who loses his position at an Italian Un= iversity and must find a new way to make a living. To quote from the Film S= ociety of Lincoln Center's website: "A band of brilliant unemployed and underemployed academics=97two Latinists= , a chemist, a neurobiologist, an anthropologist, and an economist=97turn t= o a life of crime in order to survive. Deftly assimilating such influences = as Breaking Bad and Trainspotting, this biting parody on the plight of the = Italian middle class in the aftermath of the economic crisis boasts a fast = pace, witty dialogue, and a terrific cast. A debut to watch from Salerno-na= tive Sibilia, the film was a resounding commercial and critical hit when re= leased in Italy earlier this year." I saw it yesterday. It was great fun. So if you live in the NYC area and ha= ve the time, I highly recommend it. Best, Frank Dr. Francis T. Marchese Professor Dept. of Computer Science Pace University 163 William Street, 2nd Floor New York, NY 10038 http://csis.pace.edu/~marchese email: fmarchese=pace.edu phone: 212 346-1803 Co-director, Pace Digital Gallery http://www.pace.edu/DigitalGallery --_000_7E2BCCBD9F13D747B02B65E69417735C482204C6exchnycmbx01pac_ Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable
All,

This movie recommendation may arrive a bit late, but there is one more show= ing (Sunday at 9PM) of a recent Italian comedy "I Can Quit Whenever I = Want (Smetto Quando Voglio) at the Walter Reade Theater in Lincoln Center (= new York City). See link: http://www.filmlinc.com/films/on-sale/i-can-quit-= whenever-i-want.

It is about a computational chemist who loses his position at an Italian Un= iversity and must find a new way to make a living. To quote from the Film S= ociety of Lincoln Center's website:

"A band of brilliant unemployed and underemployed academics=97two Lati= nists, a chemist, a neurobiologist, an anthropologist, and an economist=97t= urn to a life of crime in order to survive. Deftly assimilating such influe= nces as Breaking Bad and Trainspotting, this biting parody on the plight of the Italian middle class in the aftermath o= f the economic crisis boasts a fast pace, witty dialogue, and a terrific ca= st. A debut to watch from Salerno-native Sibilia, the film was a resounding= commercial and critical hit when released in Italy earlier this year."

I saw it yesterday. It was great fun. So if you live in the NYC area and ha= ve the time, I highly recommend it.

Best,
Frank

Dr. Francis T. Marchese

Professor
Dept. of Computer Science
Pace University
163 William Street, 2nd Floor
New York, NY 10038
http://csis.pace.edu/~marchese
email: fmarchese=pace.edu
phone: 212 346-1803

Co-director, Pace Digital Gallery
http://www.pace.edu/DigitalGallery

--_000_7E2BCCBD9F13D747B02B65E69417735C482204C6exchnycmbx01pac_-- From owner-chemistry@ccl.net Sat Jun 7 18:03:00 2014 From: "Paul Hawkins phawkins{:}eyesopen.com" To: CCL Subject: CCL: Looking for a conformer generator program Message-Id: <-50185-140607142718-31247-Sy98B3Vq+Z2Yre6NIXrOWg-.-server.ccl.net> X-Original-From: Paul Hawkins Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Sat, 7 Jun 2014 18:27:10 +0000 MIME-Version: 1.0 Sent to CCL by: Paul Hawkins [phawkins * eyesopen.com] Gustavo, We'll look into this and reply next week. Paul. Sent from my iPad > On Jun 6, 2014, at 4:59 PM, "GUSTAVO LAUREANO COELHO DE MOURA gustavo.moura**ufpe.br" wrote: > > > Dear Paul, > Your suggestion of using OMEGA was very interesting considering that exactly two weeks ago (on may 22nd) I applied for an academic license of OMEGA, and so far, the only answer I got from OpenEye was that you were unable to access our departmental homepage to confirm my academic status. Could you have a look on my application to see what is happening? As I explained in my application, I am a new faculty member in this university and I still do not have my own page in our departmental homepage. However, my name is listed as a professor of the department of chemistry in > http://www.dqf.ufpe.br/index.php?option=com_content&view=article&id=206&Itemid=247 > Do you suggest that I ask for a senior faculty to apply for a license? > Thank you very much in advance. > Sincerely yours, > Gustavo L.C. Moura > ----- Mensagem original ----- > > De: "Paul Hawkins phawkins]=[eyesopen.com" > Para: "Gustavo L.C. Moura " > Enviadas: Sexta-feira, 6 de junho de 2014 7:13:50 > Assunto: CCL: Looking for a conformer generator program > > > Sent to CCL by: Paul Hawkins [phawkins[a]eyesopen.com] > Omega from OpenEye Scientific fulfills your requirements; we have extended MMFF94 to be able to handle Se and OH and NH rotor sampling was recently added. > > Please visit http://www.eyesopen.com/omega for more information. > > > > Paul. > > Sent from my iPad > >> On Jun 6, 2014, at 2:45 AM, "Gustavo L.C. Moura gustavo.moura*_*ufpe.br" wrote: >> >> >> Sent to CCL by: "Gustavo L.C. Moura" [gustavo.moura=ufpe.br] >> Dear CCL community, >> I have been searching for a conformer generator program that can handle acyclic compounds (none of my molecules have flexible rings, yet). I have already tested a few programs, and so far, none has worked to my satisfaction. The program I am looking for should obey some requirements. The requirements are: >> 1) The program should use the RMSD of the coordinates to check for equivalent conformers. The first program that I tested employed only the energy to differentiate conformers and was unable to differentiate non-superimposable conformers that happen to have the same energy. >> 2) I am not overly concerned with the quality of the molecular mechanics forcefield that will be employed by the program to optimize the geometries of the conformers because I will reoptimize them with quantum chemical methods. However, I need to have a forcefield that is able to handle selenium atoms. >> 3) The program should be capable of generating conformers resulting from the rotation around C-OH and C-NH2 bonds. My interest is in the spectroscopic properties (UV-VIS and NMR) of my molecules and rotations around such bonds are very important to me. >> So, does anyone on the list know of a conformer generator program that has the characteristics above? >> Thank you very much in advance. >> Sincerely yours, >> Gustavo L.C. Mourahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt------=_Part_2663045_445858081.1402063763165 > Content-Type: text/html; charset=utf-8 > Content-Transfer-Encoding: quoted-printable > > <= > div style=3D'font-family: verdana,helvetica,sans-serif; font-size: 10pt; co= > lor: #000000'> > >

S">Dear Paul,

> >

S">Your suggestion > of using OMEGA was very interesting considering that exactly two weeks ago = > (on may > 22nd) I applied for an academic license of OMEGA, and so far, the only answ= > er I > got from OpenEye was that you were unable to access our departmental homepa= > ge > to confirm my academic status. Could you have a look on my application to s= > ee > what is happening? As I explained in my application, I am a new faculty mem= > ber > in this university and I still do not have my own page in our departmental > homepage. However, my name is listed as a professor of the department of > chemistry in

> >

S">http://www.dqf.ufpe.br/index.php?option=3Dcom_content&view=3Darticle= > &id=3D206&Itemid=3D247

> >

S">Do you > suggest that I ask for a senior faculty to apply for a license?

> >

S">Thank you > very much in advance.

> >

S">Sincerely > yours,

> >

S">      &nbs= > p;            &= > nbsp;           Gu= > stavo L.C. > Moura

> >

S"> 

> >
nt-style:normal;text-decoration:none;font-family:Helvetica,Arial,sans-serif= > ;font-size:12pt;">De: "Paul Hawkins phawkins]=3D[eyesopen.com" <o= > wner-chemistry/a\ccl.net>
Para: "Gustavo L.C. Moura " &l= > t;gustavo.moura/a\ufpe.br>
Enviadas: Sexta-feira, 6 de junho de = > 2014 7:13:50
Assunto: CCL: Looking for a conformer generator prog= > ram


Sent to CCL by: Paul Hawkins [phawkins[a]eyesopen.com]
Om= > ega from OpenEye Scientific fulfills your requirements; we have extended MM= > FF94 to be able to handle Se and OH and NH rotor sampling was recently adde= > d.

Please visit http://www.eyesopen.com/omega for more information.<= > br>


Paul.

Sent from my iPad

> On Jun 6, 2014, a= > t 2:45 AM, "Gustavo L.C. Moura gustavo.moura*_*ufpe.br" <owner-chemistry= > -,-ccl.net> wrote:
>
>
> Sent to CCL by: "Gustavo L.= > C. Moura" [gustavo.moura=3Dufpe.br]
> Dear CCL community,
> I h= > ave been searching for a conformer generator program that can handle acycli= > c compounds (none of my molecules have flexible rings, yet). I have already= > tested a few programs, and so far, none has worked to my satisfaction. The= > program I am looking for should obey some requirements. The requirements a= > re:
>    1) The program should use the RMSD of the coordina= > tes to check for equivalent conformers. The first program that I tested emp= > loyed only the energy to differentiate conformers and was unable to differe= > ntiate non-superimposable conformers that happen to have the same energy. r>>    2) I am not overly concerned with the quality of the mo= > lecular mechanics forcefield that will be employed by the program to optimi= > ze the geometries of the conformers because I will reoptimize them with qua= > ntum chemical methods. However, I need to have a forcefield that is able to= > handle selenium atoms.
>    3) The program should be capab= > le of generating conformers resulting from the rotation around C-OH and C-N= > H2 bonds. My interest is in the spectroscopic properties (UV-VIS and NMR) o= > f my molecules and rotations around such bonds are very important to me.> > So, does anyone on the list know of a conformer generator program tha= > t has the characteristics above?
> Thank you very much in advance.> > Sincerely yours,
>        Gustavo L.C. Mour= > a>
>



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