> Date: Tuesday, August 3, 2010, 4:28 AM > > > Sent to CCL by: "Guilherme Lu s Cordeiro" [guilhermecord[]gmail.com] > Dear CCL members, > > I'd like to know how valid is a scale factor. Actually, I am interested in > analysing the vibrational normal modes of two flavonoids(baicalein and > naringenin), so I did a frequency job at B3LYP level. I know that Guassian > do compute the frequency numbers from force constants, but is it necessary > to use a scale factor for comparisons between experimental and theoretical > data? And where do these scale factors come from? I would appreciate any > help and also any article quotations about scale factors. > > Regards, > Guilherme. > guilhermecord=gmail.com > Brazil, So Paulo> the strange characters on the top line to the %x% sign. You can also > E-mail to subscribers: CHEMISTRY%x%ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST%x%ccl.net or use> > > > --0016e6d5096cd33f1e048cf02d62 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable hi guilherme:

go to c= ccdbd.nist.gov and click on III. Calculated Data. =A0next, go to sectio= n B.

cheri

cccbdb =3D computational chem= istry comparison benchmard database.

On Tue, Aug 3, 2010 = at 11:28 AM, Morad El-Hendawy m80elhendawy*yah= oo.com <owner-chemistry.:.ccl.net> wrote:

Dear= Guilherme:
The calculated frequencies is scaled through multiplying them by a given factor to match with those obtained from the experiment. However, other stu= dies suggest that a dual scaling (low and high frequencies) is more effective. Please see this paper:
Theor. Chem Acc vol 105, pp 413 (2001).
Regards,
Morad El-Hendawy

---= On Tue, 8/3/10, Guilherme Lu s Cordeiro guilhermecord---gmail.com <owner-= chemistry%x%ccl.net> wrote:

From: Guilherme Lu s Cordeiro guilhermecord---gmail.com <= owner-chemistry%x%ccl.net&= gt;
Subject: CCL: Scale factor in frequency jobs
To: "El-Hendawy, Morad= Metwally " <m80elhendawy%x%yahoo.com>
Date: Tuesday, August 3, 2010, 4:28 AM

Sent to CCL by: "Guilherme Lu=A0 s Cordeiro" [guilhermec= ord[]gmail.com]
Dear = CCL members,

I'd like to know how valid is a scale factor. Actua= lly, I am interested in analysing the vibrational normal modes of two flavo= noids(baicalein and naringenin), so I did a frequency job at B3LYP level. I= know that Guassian do compute the frequency numbers from force constants, = but is it necessary to use a scale factor for comparisons between experimental and t= heoretical data? And where do these scale factors come from? I would apprec= iate any help and also any article quotations about scale factors.

Regards,
Guilherme.
guilhermecord=3Dgmail.com
Brazil, So Paulo

-=3D Thi= s is automatically added to each message by the mailing script =3D-
To r= ecover the email address of the author of the message, please change
the strange characters on the top line to the %x% sign. You can also
E-m= ail to subscribers: CHEMISTRY%x%ccl.net or use:
=A0 =A0 =A0 ht= tp://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST%x%ccl.net or use
= =A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/send_ccl_message
=A0 = =A0 =A0 http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conferences/<= br>
Search Messages: http://www.ccl.net/chemistry/searchccl/index.sht= ml
=A0 =A0 =A0 http://www.ccl.net/spammers.txt

= RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/

--0016e6d5096cd33f1e048cf02d62-- From owner-chemistry@ccl.net Tue Aug 3 16:17:01 2010 From: "William Wei william.wei|,|utoronto.ca" To: CCL Subject: CCL: Chemical database 2d to 3D convertion Message-Id: <-42417-100803152828-4020-vLTdYrR+gURSBNfHUFnERg[*]server.ccl.net> X-Original-From: "William Wei" Date: Tue, 3 Aug 2010 15:28:27 -0400 Sent to CCL by: "William Wei" [william.wei*utoronto.ca] Hi everybody, I am looking for a 2D to 3D sdf format convert software. Better if it is free. My request is if chiral center(s) in the 2D structure did not specified, I need both S and R conformation. I used Concord, but it just generate one conformation if the chiral center is not specified. If any of you have used other software can do the job, please let me know. Any information if appreciated. Thanks, William From owner-chemistry@ccl.net Tue Aug 3 16:52:00 2010 From: "Irena Efremenko irena.efremenko,weizmann.ac.il" To: CCL Subject: CCL: Scale factor in frequency jobs Message-Id: <-42418-100803163147-26852-l83xR0quMRdR1i/T7VXnyQ^server.ccl.net> X-Original-From: Irena Efremenko Content-Type: multipart/alternative; boundary=Apple-Mail-13--234897183 Date: Tue, 3 Aug 2010 23:31:37 +0300 Mime-Version: 1.0 (Apple Message framework v1081) Sent to CCL by: Irena Efremenko [irena.efremenko,,weizmann.ac.il] --Apple-Mail-13--234897183 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii The most recent article on the subject: Scaling Factors and Uncertainties for ab Initio Anharmonic Vibrational = Frequencies. Russell D. Johnson, III, Karl K. Irikura, Raghu N. Kacker = and Rdiger Kessel. J. Chem. Theory Comput., Article ASAP DOI: 10.1021/ct100244d http://pubs.acs.org/doi/full/10.1021/ct100244d=20 ****** Dr. Irena Efremenko Department of Organic Chemistry Weizmann Institute of Science 76100 Rehovot, Israel Phone: +972 8 9343680 FAX: +972 8 9344142 Email: irena.efremenko[*]weizmann.ac.il ****** On Aug 3, 2010, at 10:18 PM, Cheri McFerrin cmcfer1#,#tigers.lsu.edu = wrote: > hi guilherme: >=20 > go to cccdbd.nist.gov and click on III. Calculated Data. next, go to = section B. >=20 > cheri > cccbdb =3D computational chemistry comparison benchmard database. >=20 >=20 >=20 > On Tue, Aug 3, 2010 at 11:28 AM, Morad El-Hendawy = m80elhendawy*yahoo.com wrote: > Dear Guilherme: > The calculated frequencies is scaled through multiplying them by a = given > factor to match with those obtained from the experiment. However, = other studies suggest that a dual scaling (low and high frequencies) is = more effective. Please see this paper: > Theor. Chem Acc vol 105, pp 413 (2001). > Regards, > Morad El-Hendawy >=20 >=20 >=20 > --- On Tue, 8/3/10, Guilherme Lu s Cordeiro guilhermecord---gmail.com = wrote: >=20 > From: Guilherme Lu s Cordeiro guilhermecord---gmail.com = > Subject: CCL: Scale factor in frequency jobs > To: "El-Hendawy, Morad Metwally " > Date: Tuesday, August 3, 2010, 4:28 AM >=20 >=20 > Sent to CCL by: "Guilherme Lu s Cordeiro" [guilhermecord[]gmail.com] > Dear CCL members, >=20 > I'd like to know how valid is a scale factor. Actually, I am = interested in analysing the vibrational normal modes of two = flavonoids(baicalein and naringenin), so I did a frequency job at B3LYP = level. I know that Guassian do compute the frequency numbers from force = constants, but is it necessary to use a scale factor for comparisons = between experimental and theoretical data? And where do these scale = factors come from? I would appreciate any help and also any article = quotations about scale factors. >=20 > Regards, > Guilherme. > guilhermecord=3Dgmail.com > Brazil, So Paulo >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change > the strange characters on the top line to the %x% sign. You can also > E-mail to subscribers: CHEMISTRY%x%ccl.net or use:>=20 > E-mail to administrators: CHEMISTRY-REQUEST%x%ccl.net or use>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20 >=20>=20>=20 >=20 >=20 >=20 --Apple-Mail-13--234897183 Content-Transfer-Encoding: 7bit Content-Type: text/html; charset=us-ascii The most recent article on the subject:

Scaling Factors and Uncertainties for ab Initio Anharmonic Vibrational Frequencies. Russell D. Johnson, III, Karl K. Irikura, Raghu N. Kacker and R

diger Kessel.

J. Chem. Theory Comput., Article ASAP

DOI: 10.1021/ct100244d

http://pubs.acs.org/doi/full/10.1021/ct100244d

******
Dr. Irena Efremenko
Department of Organic Chemistry
Weizmann Institute of Science
76100 Rehovot, Israel
Phone: +972 8 9343680
FAX: +972 8 9344142
Email: irena.efremenko[*]weizmann.ac.il
******

On Aug 3, 2010, at 10:18 PM, Cheri McFerrin cmcfer1#,#tigers.lsu.edu wrote:

hi guilherme:

go to cccdbd.nist.gov and click on III. Calculated Data. next, go to section B.

cheri
cccbdb = computational chemistry comparison benchmard database.

On Tue, Aug 3, 2010 at 11:28 AM, Morad El-Hendawy m80elhendawy*yahoo.com <owner-chemistry[A]ccl.net> wrote:

Dear Guilherme:
The calculated frequencies is scaled through multiplying them by a given
factor to match with those obtained from the experiment. However, other studies suggest that a dual scaling (low and high frequencies) is more effective. Please see this paper:
Theor. Chem Acc vol 105, pp 413 (2001).
Regards,
Morad El-Hendawy

--- On Tue, 8/3/10, Guilherme Lu s Cordeiro guilhermecord---gmail.com <owner-chemistry%x%ccl.net> wrote:

From: Guilherme Lu s Cordeiro guilhermecord---gmail.com <owner-chemistry%x%ccl.net>
Subject: CCL: Scale factor in frequency jobs
To: "El-Hendawy, Morad Metwally " <m80elhendawy%x%yahoo.com>
Date: Tuesday, August 3, 2010, 4:28 AM

Sent to CCL by: "Guilherme Lu s Cordeiro" [guilhermecord[]gmail.com]
Dear CCL members,

I'd like to know how valid is a scale factor. Actually, I am interested in analysing the vibrational normal modes of two flavonoids(baicalein and naringenin), so I did a frequency job at B3LYP level. I know that Guassian do compute the frequency numbers from force constants, but is it necessary to use a scale factor for comparisons between experimental and theoretical data? And where do these scale factors come from? I would appreciate any help and also any article quotations about scale factors.

Regards,
Guilherme.
guilhermecord=gmail.com
Brazil, So Paulo

the strange characters on the top line to the %x% sign. You can also
E-mail to subscribers: CHEMISTRY%x%ccl.net or use:
http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST%x%ccl.net or use
http://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml

http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/

--Apple-Mail-13--234897183-- From owner-chemistry@ccl.net Tue Aug 3 17:26:01 2010 From: "Mahmoud A. A. Ibrahim m.ibrahim(~)compchem.net" To: CCL Subject: CCL: charmm energy Message-Id: <-42419-100803165947-30035-K8wgSODFPx0usDUPH/zwoQ#%#server.ccl.net> X-Original-From: "Mahmoud A. A. Ibrahim" Content-Type: multipart/alternative; boundary=001636459018517b42048cf1984e Date: Tue, 3 Aug 2010 21:59:37 +0100 MIME-Version: 1.0 Sent to CCL by: "Mahmoud A. A. Ibrahim" [m.ibrahim..compchem.net] --001636459018517b42048cf1984e Content-Type: text/plain; charset=KOI8-R Content-Transfer-Encoding: quoted-printable Dear Tatsiana I don't know what the default method is used when you don't specify gb "-pa= r gb". All what I can do is to inform you that this may be returned to the atomic radii used during the calculation, "different radii give different binding energies In addition to the equation used for solvation free enegy calculation and electrostatic contribution. Sure, Eele will be different, for example, in case of "gb" the software uses Generalized Born equation, and in case of th= e default option the software uses another equation like Poisson Boltzmann equation, this leads to a variation in the binding energy too. For just a thread to follow: "Converging Free Energy Estimates: MM-PB(GB)SA Studies on the Protein-Protein Complex Ras-Raf" Hope it may be helpful Sincerely; M. Ibrahim in addition to the equation used for solvation free energy calculation "Generalized Born in case of GB, or another Tatsiana 2010/8/3 Tatsiana Kirys nushki~~mail.ru > > Sent to CCL by: Tatsiana Kirys [nushki!=3D!mail.ru] > > I posted it to MMTSB forum at charmm.org ( > http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=3Dshowflat&Numb= er=3D24980#Post24980 > ) > > but nobody answers it. > > I'd appreciate your help! > > Tatsiana Kirys > PhD student in bioinformatics > > Thu, 29 Jul 2010 18:23:24 -0400 =D0=C9=D3=D8=CD=CF =CF=D4 "Venable, Richa= rd (NIH/NHLBI) E > venabler^^^nhlbi.nih.gov" : > > > > > Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler:+: > nhlbi.nih.gov] > > I suggest posting your question to the MMTSB forum at www.charmm.org > > > > -- > > Rick Venable 5635 FL/T906 > > Membrane Biophysics Section > > NIH/NHLBI Lab. of Computational Biology > > Bethesda, MD 20892-9314 U.S.A. > > > > > > On 7/29/10 4:40 PM, "Barry Hardy barry.hardy*o*vtxmail.ch" > wrote: > > > > > > > > Sent to CCL by: "Tatsiana Kirys" [tatsiana%x%ku.edu] > > Hi all, > > > > i calculate protein energy using enrCHARMM.pl script. i run it with gb > and without for the same protein file. > > > > enerCHARMM.pl -out total -log file.log file.pdb > > BONDs 92.56954 > > ANGLes 336.00337 > > UREY-b 24.08096 > > DIHEdrals 604.46805 > > CMAPs -134.62511 > > VDWaals -476.01682 > > ELEC -2041.80015 > > > > > > enerCHARMM.pl -out total -par gb -log file_gb.log file.pdb > > > > BONDs 92.56954 > > ANGLes 336.00337 > > UREY-b 24.08096 > > DIHEdrals 604.46805 > > CMAPs -134.62511 > > VDWaals -485.01639 > > ELEC -2021.31359 > > ASP 102.42587 > > GBEnr -1479.15727 > > > > i dont understand why Electrostatic and VdW energy terms are different. > Any help will be very appreciated!!!=F1 =D7 =ED=CF=C5=CD =ED=C9=D2=C5 - > http://my.mail.ru/mail/nushki/ > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 Mahmoud A. A. Ibrahim Current Address 7.05, School of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom. Home Address Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt. Contact Information Email: m.ibrahim(-)compchem.net Website: www.compchem.net Fax No.: +20862342601 --001636459018517b42048cf1984e Content-Type: text/html; charset=KOI8-R Content-Transfer-Encoding: quoted-printable Dear Tatsiana

I don't know what the default method is us= ed when you don't specify gb "-par gb".

All what I = can do is to inform you that this may be returned to the atomic radii = used during the calculation, "different radii give different binding e= nergies

In addition to the equation used for solvation free enegy calculation = and electrostatic contribution. Sure, Eele will be different, for example, = in case of "gb" the software uses Generalized Born equation, and = in case of the default option the software uses another equation like Poiss= on Boltzmann equation, this leads to a variation in the binding energy too.=

For just a thread to follow: "Converging Free Energy Estimat= es: MM-PB(GB)SA Studies on the Protein–Protein Complex Ras&ndash= ;Raf"

Hope it may be helpful

Sincerely;

M. Ibrahim

in addition to the equation used for solvation free e= nergy calculation "Generalized Born in case of GB, or another
Tatsiana

2010/8/3 Tatsiana Kirys nushki~~mail.ru <owner-chemistry(-)ccl.net>

Sent to CCL by: Tatsiana Kirys [nushki!=3D!mail.ru]

I posted it to MMTSB forum at charmm.org (htt= p://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=3Dshowflat&Numbe= r=3D24980#Post24980)

but nobody answers it.

I'd appreciate your help!

Tatsiana Kirys
PhD student in bioinformatics

Thu, 29 Jul 2010 18:23:24 -0400 =D0=C9=D3=D8=CD=CF =CF=D4 "Venable, Ri= chard (NIH/NHLBI) E venabler^^^nhlbi.nih.gov" <owner-chemistry[a]ccl.net>:

>
> Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler= :+:nhlbi.nih.gov] > I suggest posting your question to the MMTSB forum at www.charmm.org
>
> --
> Rick Venable 5635 FL/T906
> Membrane Biophysics Section
> NIH/NHLBI Lab. of Computational Biology
> Bethesda, MD 20892-9314 U.S.A.
>
>
> On 7/29/10 4:40 PM, "Barry Hardy barry.hardy*o*vtxmail.ch" <owner-chemistry(a)ccl.net> wrote:
>
>
>
> Sent to CCL by: "Tatsiana Kirys" [tatsiana%x%ku.edu]
> Hi all,
>
> i calculate protein energy using enrCHARMM.pl script. i run it with gb= and without for the same protein file.
>
> enerCHARMM.pl -out total -log file.log file.pdb
> BONDs 92.56954
> ANGLes 336.00337
> UREY-b 24.08096
> DIHEdrals 604.46805
> CMAPs -134.62511
> VDWaals -476.01682
> ELEC -2041.80015
>
>
> enerCHARMM.pl -out total -par gb -log file_gb.log file.pdb
>
> BONDs 92.56954
> ANGLes 336.00337
> UREY-b 24.08096
> DIHEdrals 604.46805
> CMAPs -134.62511
> VDWaals -485.01639
> ELEC -2021.31359
> ASP 102.42587
> GBEnr -1479.15727
>
> i dont understand why Electrostatic and VdW energy terms are different= . Any help will be very appreciated!!!=F1 =D7 =ED=CF=C5=CD =ED=C9=D2=C5 - <= a href=3D"http://my.mail.ru/mail/nushki/" target=3D"_blank">http://my.mail.= ru/mail/nushki/

-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY(-)ccl.n= et or use:
http://www.ccl.net/cgi-bin/ccl/send_ccl_message=

E-mail to administrators: CHEM= ISTRY-REQUEST(-)ccl.net or use
http://www.ccl.net/cgi-bin/ccl/send_ccl_message=

Subscribe/Unsubscribe:
http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/

--
&n= bsp; Mahmoud A. A. Ibrahim =
&n= bsp;    Current Address
&nb= sp;    7.05, School of Chemistry,
= The University of Manchester,
   Oxford Road, Manchester, M13 9PL,
&nb= sp; &n= bsp; United Kingdom.

= ; Home Address
&= nbsp; Chemistry Department,
&n= bsp;    Faculty = of Science,
&nbs= p; Minia University,
= ;    Minia 61519,
&n= bsp; = Egypt.

&nbs= p;    Contact Information
&n= bsp; Email: m.ibrahim(-)compchem.ne= t
Website: www.compchem.net
&nbs= p;    Fax No.: +20862342601

--001636459018517b42048cf1984e-- From owner-chemistry@ccl.net Tue Aug 3 18:12:00 2010 From: "Reichert, David reichertd[a]mir.wustl.edu" To: CCL Subject: CCL: Chemical database 2d to 3D conversion Message-Id: <-42420-100803175503-1406-O0pLCxkuFFS+UJQeqEfJSg*|*server.ccl.net> X-Original-From: "Reichert, David" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 3 Aug 2010 16:54:51 -0500 MIME-Version: 1.0 Sent to CCL by: "Reichert, David" [reichertd_-_mir.wustl.edu] Hi William, If you've got academic access to the OpenEye suite of tools they've got a program called "flipper" which takes 2D input and then generates all of the stereoisomers. In general I'll run flipper on smiles strings the run the output into omega to generate reasonable 3D conformations. -david David E. Reichert, PhD. Asst. Professor of Radiology Washington University School of Medicine e-mail: reichertd]=[wustl.edu voice: 314-362-8461 fax: 314-362-9940 web: http://scoobie.wustl.edu/ -----Original Message----- > From: owner-chemistry+reichertd==mir.wustl.edu]=[ccl.net [mailto:owner-chemistry+reichertd==mir.wustl.edu]=[ccl.net] On Behalf Of William Wei william.wei|,|utoronto.ca Sent: Tuesday, August 03, 2010 02:28 PM To: Reichert, David Subject: CCL: Chemical database 2d to 3D convertion Sent to CCL by: "William Wei" [william.wei*utoronto.ca] Hi everybody, I am looking for a 2D to 3D sdf format convert software. Better if it is free. My request is if chiral center(s) in the 2D structure did not specified, I need both S and R conformation. I used Concord, but it just generate one conformation if the chiral center is not specified. If any of you have used other software can do the job, please let me know. Any information if appreciated. Thanks, Williamhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThe material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. From owner-chemistry@ccl.net Tue Aug 3 18:46:01 2010 From: "Greg Warren greg:eyesopen.com" To: CCL Subject: CCL: Chemical database 2d to 3D convertion Message-Id: <-42421-100803184210-22171-ot6J4rFeXFC3oqHCHwQR0A .. server.ccl.net> X-Original-From: Greg Warren Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 3 Aug 2010 15:42:05 -0700 MIME-Version: 1.0 Sent to CCL by: Greg Warren [greg]~[eyesopen.com] Being from a University you can apply for and receive a free academic license from OpenEye. You would need to run two programs flipper and then omega2. Flipper will enumerate unspecified chemistry (only unspecified) and omega2 will generate a 3D conformation. You can apply for a license using the following link http://www.eyesopen.com/forms/academic_license_app.php Regards, Greg -----Original Message----- > From: owner-chemistry+greg==eyesopen.com/a\ccl.net [mailto:owner-chemistry+greg==eyesopen.com/a\ccl.net] On Behalf Of William Wei william.wei|,|utoronto.ca Sent: Tuesday, August 03, 2010 1:28 PM To: Greg Warren Subject: CCL: Chemical database 2d to 3D convertion Sent to CCL by: "William Wei" [william.wei*utoronto.ca] Hi everybody, I am looking for a 2D to 3D sdf format convert software. Better if it is free. My request is if chiral center(s) in the 2D structure did not specified, I need both S and R conformation. I used Concord, but it just generate one conformation if the chiral center is not specified. If any of you have used other software can do the job, please let me know. Any information if appreciated. Thanks, Williamhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt