CCL: Looking for a conformer generator program

From: Paul Hawkins <phawkins ~ eyesopen.com>
Subject: CCL: Looking for a conformer generator program
Date: Sat, 7 Jun 2014 18:27:10 +0000
 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" <owner-chemistry###ccl.net> 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"
 <owner-chemistry/a\ccl.net>
 > Para: "Gustavo L.C. Moura " <gustavo.moura/a\ufpe.br>
 > 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" <owner-chemistry-,-ccl.net> 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
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 > <p class=3D"MsoNormal"><span
 style=3D"mso-ansi-language:EN-US" lang=3D"EN-U=
 > S">Dear Paul,</span></p>
 >
 > <p class=3D"MsoNormal"><span
 style=3D"mso-ansi-language:EN-US" lang=3D"EN-U=
 > 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</span></p>
 >
 > <p class=3D"MsoNormal"><span
 style=3D"mso-ansi-language:EN-US" lang=3D"EN-U=
 > S">http://www.dqf.ufpe.br/index.php?option=3Dcom_content&amp;view=3Darticle=
 > &amp;id=3D206&amp;Itemid=3D247</span></p>
 >
 > <p class=3D"MsoNormal"><span
 style=3D"mso-ansi-language:EN-US" lang=3D"EN-U=
 > S">Do you
 > suggest that I ask for a senior faculty to apply for a
 license?</span></p>
 >
 > <p class=3D"MsoNormal"><span
 style=3D"mso-ansi-language:EN-US" lang=3D"EN-U=
 > S">Thank you
 > very much in advance.</span></p>
 >
 > <p class=3D"MsoNormal"><span
 style=3D"mso-ansi-language:EN-US" lang=3D"EN-U=
 > S">Sincerely
 > yours,</span></p>
 >
 > <p class=3D"MsoNormal"><span
 style=3D"mso-ansi-language:EN-US" lang=3D"EN-U=
 > S"><span
 style=3D"mso-tab-count:2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
 >
 p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&=
 >
 nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
 </span>Gu=
 > stavo L.C.
 > Moura</span></p>
 >
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 > <![endif]--><hr id=3D"zwchr"><div
 style=3D"color:#000;font-weight:normal;fo=
 >
 nt-style:normal;text-decoration:none;font-family:Helvetica,Arial,sans-serif=
 > ;font-size:12pt;"><b>De: </b>"Paul Hawkins
 phawkins]=3D[eyesopen.com" &lt;o=
 > wner-chemistry/a\ccl.net&gt;<br><b>Para:
 </b>"Gustavo L.C. Moura " &l=
 > t;gustavo.moura/a\ufpe.br&gt;<br><b>Enviadas:
 </b>Sexta-feira, 6 de junho de =
 > 2014 7:13:50<br><b>Assunto: </b>CCL: Looking for a
 conformer generator prog=
 > ram<br><br><br>Sent to CCL by: Paul Hawkins
 [phawkins[a]eyesopen.com]<br>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.<br><br>Please visit http://www.eyesopen.com/omega for more information.<=
 > br><br><br><br>Paul.<br><br>Sent from my
 iPad<br><br>&gt; On Jun 6, 2014, a=
 > t 2:45 AM, "Gustavo L.C. Moura gustavo.moura*_*ufpe.br"
 &lt;owner-chemistry=
 > -,-ccl.net&gt; wrote:<br>&gt; <br>&gt;
 <br>&gt; Sent to CCL by: "Gustavo L.=
 > C. Moura" [gustavo.moura=3Dufpe.br]<br>&gt; Dear CCL
 community,<br>&gt; 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:<br>&gt; &nbsp; &nbsp;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.<b=
 > r>&gt; &nbsp; &nbsp;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.<br>&gt; &nbsp; &nbsp;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.<br=
 >> &gt; So, does anyone on the list know of a conformer generator
 program tha=
 > t has the characteristics above?<br>&gt; Thank you very much in
 advance.<br=
 >> &gt; Sincerely yours,<br>&gt; &nbsp; &nbsp;
 &nbsp; &nbsp;Gustavo L.C. Mour=
 > a&gt; <br>&gt;<br><br><br><br>-=3D
 This is automatically added to each mess=
 > age by the mailing script =3D-<br>To recover the email address of the
 autho=
 > r of the message, please change<br>the strange characters on the top
 line t=
 > o the /a\ sign. You can also<br>look up the X-Original-From: line in
 the mail=
 > header.<br><br<br>&nbsp;&=
 > nbsp; &nbsp; &nbsp;http://www.ccl.net/cgi-bin/ccl/send_ccl_message<br><br>E=
 > -mail to administrators: CHEMISTRY-REQUEST/a\ccl.net or
 use<br>&nbsp;&nbsp; &=
 > nbsp; &nbsp;http://www.ccl.net/cgi-bin/ccl/send_ccl_message<br><br>Subscrib=
 > e/Unsubscribe: <br>&nbsp;&nbsp; &nbsp; &nbsp;http://www.ccl.net/chemistry/s=
 > ub_unsub.shtml<br><br>Before posting, check wait time at: http://www.ccl.ne=
 > t<br><br<br>Conferences: http://server.ccl.ne=
 > t/chemistry/announcements/conferences/<br><br>Search Messages:
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 > cl.net/chemistry/searchccl/index.shtml<br><br>If your mail
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 > with 5.7.1 error, check:<br>&nbsp;&nbsp; &nbsp;
 &nbsp;http://www.ccl.net/s=
 > pammers.txt<br><br>RTFI: http://www.ccl.net/chemistry/aboutccl/instructions=
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 /<br><br><br></div><br></div></body></html>