From owner-chemistry@ccl.net Fri Jun 6 07:51:00 2014 From: "Paul Hawkins phawkins]=[eyesopen.com" To: CCL Subject: CCL: Looking for a conformer generator program Message-Id: <-50178-140606061357-2066-RqaXVAH7qzpJaWbBFc/Wrg^^server.ccl.net> X-Original-From: Paul Hawkins Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 6 Jun 2014 10:13:50 +0000 MIME-Version: 1.0 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. Moura> > From owner-chemistry@ccl.net Fri Jun 6 10:57:00 2014 From: "GUSTAVO LAUREANO COELHO DE MOURA gustavo.moura**ufpe.br" To: CCL Subject: CCL: Looking for a conformer generator program Message-Id: <-50179-140606101127-5478-cAxdac+z2cmC44+ppphDfg|server.ccl.net> X-Original-From: GUSTAVO LAUREANO COELHO DE MOURA Content-Type: multipart/alternative; boundary="----=_Part_2663045_445858081.1402063763165" Date: Fri, 6 Jun 2014 11:09:23 -0300 (BRT) MIME-Version: 1.0 Sent to CCL by: GUSTAVO LAUREANO COELHO DE MOURA [gustavo.moura=-=ufpe.br] ------=_Part_2663045_445858081.1402063763165 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 7bit 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'>

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 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

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

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

Thank you very much in advance.

Sincerely yours,

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

 

De: "Paul Hawkins phawkins]=3D[eyesopen.com" <o= wner-chemistry===ccl.net>
Para: "Gustavo L.C. Moura " &l= t;gustavo.moura===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.>    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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------=_Part_2663045_445858081.1402063763165-- From owner-chemistry@ccl.net Fri Jun 6 14:49:00 2014 From: "Carsten Detering detering]*[biosolveit.de" To: CCL Subject: CCL: Release Announcement: Ammunition for all drug hunters Message-Id: <-50180-140606144521-12065-0QggVih4A0A3ONbozeSTCg _ server.ccl.net> X-Original-From: "Carsten Detering" Date: Fri, 6 Jun 2014 14:45:20 -0400 Sent to CCL by: "Carsten Detering" [detering() biosolveit.de] Visualize Your SAR! Free Energy-Driven Lead Optimization for Medicinal Chemistry Dear Scientists, SeeSAR is a new, cutting edge software tool tailor-made for all drug hunters who want to prioritize their ideas fast. We guarantee: You have never seen anything easier to use in chemistry. 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From owner-chemistry@ccl.net Fri Jun 6 15:50:00 2014 From: "Geoffrey Hutchison geoffh++pitt.edu" To: CCL Subject: CCL: Looking for a conformer generator program Message-Id: <-50181-140606154726-5907-Qi9LyZYiMyWKxDy1JdWCNg^^^server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Fri, 6 Jun 2014 15:47:19 -0400 Mime-Version: 1.0 (Mac OS X Mail 7.3 \(1878.2\)) Sent to CCL by: Geoffrey Hutchison [geoffh()pitt.edu] There are several good conformer programs, and you haven't mentioned which ones you've used. OMEGA it seems, might meet your needs. Not surprisingly, I'd humbly suggest you take a look at Open Babel (http://openbabel.org/) or RDKit. (Full disclosure.. I develop Open Babel.) > 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. Open Babel allows multiple conformer criteria, including energy or RMSD. http://open-babel.readthedocs.org/en/latest/Command-line_tools/babel.html#generating-conformers-for-structures > 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. As mentioned, Open Eye has extended MMFF94 to some selenium species. While OB's MMFF94 implementation does not offer this extension, Open Babel also supports UFF, which supports Se and many other elements. > 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. In most conformer generators, it's possible to edit some templates to specify rotatable bonds. Moreover, as open source, it's not hard to hack (or find someone to hack) appropriate rotors like -C-OH or -C-NH2. I also know that RDKit (http://rdkit.org/) offers MMFF94 (without Se) and UFF and the distance geometry method is extremely effective at generating conformers, including rotors like COH and CNH2. Again, it's open source if it doesn't precisely meet your needs. Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh#pitt.edu web: http://hutchison.chem.pitt.edu/ From owner-chemistry@ccl.net Fri Jun 6 22:58:00 2014 From: "GUSTAVO LAUREANO COELHO DE MOURA gustavo.moura]*[ufpe.br" To: CCL Subject: CCL: Looking for a conformer generator program Message-Id: <-50182-140606210539-1545-YJqBPGjX9+9KAv6RN8fKFA#server.ccl.net> X-Original-From: GUSTAVO LAUREANO COELHO DE MOURA Content-Type: multipart/alternative; boundary="----=_Part_2777125_343280365.1402102757522" Date: Fri, 6 Jun 2014 21:59:17 -0300 (BRT) MIME-Version: 1.0 Sent to CCL by: GUSTAVO LAUREANO COELHO DE MOURA [gustavo.moura*ufpe.br] ------=_Part_2777125_343280365.1402102757522 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 7bit Dear Geoffrey, I am now trying to test your suggestion of using Open Babel. Unfortunately, I am having problems to generate conformers with Open Babel. Most likely I am doing something wrong, but I do not know what my mistake is. My steps were: 1) First, I performed a fresh installation of Open Babel on my Windows notebook (I have downloaded the version that comes with the GUI). 2) Next I prepared an SDF file with an initial geometry for the methyl ethyl ether (a molecule that has only three simple conformations). 3) Then I went to the command line and typed: obabel initial.sdf -O final.sdf --conformer --systematic However, the program generated the file final.sdf that contained only the input geometry (from initial.sdf). Could you help me identifying what my mistake is? Thank you very much in advance. Sincerely yours, Gustavo L.C. Moura ----- Mensagem original ----- De : "Geoffrey Hutchison geoffh++pitt.edu" Para: "Gustavo L.C. Moura " Enviadas: Sexta-feira, 6 de junho de 2014 16:47:19 Assunto : CCL: Looking for a conformer generator program Sent to CCL by: Geoffrey Hutchison [geoffh()pitt.edu] There are several good conformer programs, and you haven't mentioned which ones you've used. OMEGA it seems, might meet your needs. Not surprisingly, I'd humbly suggest you take a look at Open Babel (http://openbabel.org/) or RDKit. (Full disclosure.. I develop Open Babel.) > 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. Open Babel allows multiple conformer criteria, including energy or RMSD. http://open-babel.readthedocs.org/en/latest/Command-line_tools/babel.html#generating-conformers-for-structures > 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. As mentioned, Open Eye has extended MMFF94 to some selenium species. While OB's MMFF94 implementation does not offer this extension, Open Babel also supports UFF, which supports Se and many other elements. > 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. In most conformer generators, it's possible to edit some templates to specify rotatable bonds. Moreover, as open source, it's not hard to hack (or find someone to hack) appropriate rotors like -C-OH or -C-NH2. I also know that RDKit (http://rdkit.org/) offers MMFF94 (without Se) and UFF and the distance geometry method is extremely effective at generating conformers, including rotors like COH and CNH2. Again, it's open source if it doesn't precisely meet your needs. Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel : (412) 648-0492 email : geoffh+/-pitt.edu web : http://hutchison.chem.pitt.edu/http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt------=_Part_2777125_343280365.1402102757522 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'>

Dear Geoffrey,

I am now trying to test your suggestion of using Ope= n Babel. Unfortunately, I am having problems to generate conformers with Open Babel. Most likely I am doing something wrong, but I do not know what my mistake i= s. My steps were:

1)  <= /span>First, I performed a fresh installation of Open Babel on my Windows notebook (I have downloade= d the version that comes with the GUI).

2)  Next I prepared an SDF file with an initial geometry for the methyl ethyl ether (a molecule that has only three simple = conformations).

3)  <= /span>Then I went to the command line and typed:

obabel initial.sd= f -O final.sdf --conformer --systematic

However, the program generated the file final.sdf th= at contained only the input geometry (from initial.sdf).

Could you help me identifying what my mistake is?

Thank you very much in advance.

Sincerely yours,

   &n= bsp;            = ;            &n= bsp;   Gustavo L.C. Moura


De: "Geoffrey Hutchison geoffh++pitt.e= du" <owner-chemistry/a\ccl.net>
Para: "Gustavo L.C. Moura -id= #44f-" <gustavo.moura/a\ufpe.br>
Enviadas: Sexta-feira, 6 de = junho de 2014 16:47:19
Assunto: CCL: Looking for a confor= mer generator program


Sent to CCL by: Geoffrey Hutchison [geoffh= ()pitt.edu]
There are several good conformer programs, and you haven't m= entioned which ones you've used. OMEGA it seems, might meet your needs.
=
Not surprisingly, I'd humbly suggest you take a look at Open Babel (htt= p://openbabel.org/) or RDKit. (Full disclosure.. I develop Open Babel.)
=
>         1) The program sho= uld use the RMSD of the coordinates to check for equivalent conform= ers. The first program that I tested employed only the energy to di= fferentiate conformers and was unable to differentiate non-superimposable<= /span> conformers that happen to have the same energy.

Open Babel al= lows multiple conformer criteria, including energy or RMSD.
http://open-= babel.readthedocs.org/en/latest/Command-line_tools/babel.html#generating-co= nformers-for-structures

>       &nb= sp; 2) I am not overly concerned with the quality of the molecular mec= hanics forcefield that will be employed by the program to optimize = the geometries of the conformers because I will reoptimize them wit= h quantum chemical methods. However, I need to have a forcefield th= at is able to handle selenium atoms.

As mentioned, Open Eye has exte= nded MMFF94 to some selenium species. While OB's MMFF94 implementation does= not offer this extension, Open Babel also supports UFF, which supports Se = and many other elements.

>       &n= bsp; 3) The program should be capable of generating conformers resulti= ng from the rotation around C-OH and C-NH2 bonds. My interest is in the spe= ctroscopic properties (UV-VIS and NMR) of my molecules and rotations around= such bonds are very important to me.

In most conformer generators, = it's possible to edit some templates to specify rotatable bonds. Mo= reover, as open source, it's not hard to hack (or find someone to hack) app= ropriate rotors like -C-OH or -C-NH2.


I also know that RDKit (ht= tp://rdkit.org/) offers MMFF94 (without Se) and UFF and the distance geomet= ry method is extremely effective at generating conformers, including rotors= like COH and CNH2. Again, it's open source if it doesn't precisely meet yo= ur needs.



Hope that helps,
-Geoff


---
Prof.= Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh<= br>tel: (412) 648-0492
email: geoffh+/-pitt.edu
web<= /span>: http://hutchison.chem.pitt.edu/



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