From owner-chemistry@ccl.net Tue Jan 10 13:03:00 2006 From: "Avital Steinberg steinbergavital===gmail.com" To: CCL Subject: CCL:G: Solution-phase geometry optimization Message-Id: <-30452-060110045245-7114-1dsOW4BgeyDb/slBg8DKHA%a%server.ccl.net> X-Original-From: Avital Steinberg Content-Type: multipart/alternative; boundary="----=_Part_64385_27539802.1136883363883" Date: Tue, 10 Jan 2006 10:56:03 +0200 MIME-Version: 1.0 Sent to CCL by: Avital Steinberg [steinbergavital|a|gmail.com] ------=_Part_64385_27539802.1136883363883 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi Chris, Thank you for your answer - I've been having trouble getting my optimizations to converge using the PCM model in Gaussian03 too. I would like to use SMxGAUSS with Gaussian03 output files of the converged gas phas= e calculations. I looked at the link but I did not understand which platforms this program works with. I prefer Windows but if it's impossible, I can use Linux (not Red Hat - some other less common distribution), or a G4 Mac with system 9 & 10 operating systems. Will any of these platforms work with this program? Thanks, Avital On 1/9/06, Christopher Cramer cramer . chem.umn.edu wrote: > > Sent to CCL by: Christopher Cramer [cramer*o*chem.umn.edu] > > --Apple-Mail-5--396687927 > Content-Transfer-Encoding: 7bit > Content-Type: text/plain; > charset=3DUS-ASCII; > delsp=3Dyes; > format=3Dflowed > > Jianing, > > The SMx solvation models have nice, stable gradients and optimize > efficiently. For instance, Christopher Hadad noted in a JACS paper a > few years back that he found optimization of sugar geometries > impossible with other solvation models but had no problem with SMx. > > While we are still waiting for G03 to make SMx models available (and > by waiting I don't mean that I expect it to happen anytime soon), the > models are available in HONDOPLUS, GAMESSPLUS, and SMxGAUSS. The > latter program is of particular use to Gaussian 03 users as it can be > invoked with the Gaussian "external" keyword. For those with already > generated output files from the gas phase, SMxGAUSS also has Gaussian > formatted input files and can parse Gaussian output to run > independently. > > Full details on the various software packages (all of which are free) > can be found at > > http://comp.chem.umn.edu/smxgauss/ > http://comp.chem.umn.edu/hondoplus/ > http://comp.chem.umn.edu/gamessplus/ > > Best regards, > > Chris > > On Jan 9, 2006, at 9:18 AM, Jianing Li jianing810[#]gmail.com wrote: > > > Sent to CCL by: "Jianing Li" [jianing810 _ gmail.com] > > Dear All, > > I have a question about the geometry optimization in solutions. I > > am eager to know a reliable and effective method to deal with the > > solution-phase optimization. I am using Gaussian03 but the > > difference in geometry is not as significant as we guess when > > comparing the optimization in solution-phase and in gas-phase. > > What's more, there are two problems of solution-phase optimization: > > 1) It is very time-consuming to pursue optimization in solutions. > > 2) It is hard to obtain the convergence. I am always frustrated to > > find the unconvergence after several days' optimizing. And during > > those convergent geometries, there are always small imaginary > > frequencies. > > > > I know it is very controversial about the necessity of solution- > > phase optimization, and I am wondering whether there is any > > solution to solve this problem. Does anyone know the related > > software or any tricks to do it in Gaussian? > > > > Thanks a lot. > > > > Sincerely yours, > > Jianing > > > > > > > > -=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> > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > > search)> > > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > > +-+-+ > > > > > > > > -- > > Christopher J. Cramer > University of Minnesota > Department of Chemistry > 207 Pleasant St. SE > Minneapolis, MN 55455-0431 > -------------------------- > Phone: (612) 624-0859 || FAX: (612) 626-2006 > Mobile: (952) 297-2575 > cramer|,|pollux.chem.umn.edu > http://pollux.chem.umn.edu/~cramer > (website includes information about the textbook "Essentials > of Computational Chemistry: Theories and Models, 2nd Edition") > > > --Apple-Mail-5--396687927 > Content-Transfer-Encoding: quoted-printable > Content-Type: text/html; > charset=3DISO-8859-1 > > -khtml-line-break: after-white-space; ">Jianing,

class=3D3D"khtml-block-placeholder">
The SMx solvation models = =3D > have nice, stable gradients and optimize efficiently. For instance, =3D > Christopher Hadad noted in a JACS paper a few years back that he found = =3D > optimization of sugar geometries impossible with other solvation models = =3D > but had no problem with SMx.

class=3D3D"khtml-block-placeholder">
While we are still waiting= =3D > for G03 to make SMx models available (and by waiting I don't mean that I = =3D > expect it to happen anytime soon), the models are available in =3D > HONDOPLUS, GAMESSPLUS, and SMxGAUSS. The latter program is of particular = =3D > use to Gaussian 03 users as it can be invoked with the Gaussian =3D > "external" keyword. For those with already generated output files from = =3D > the gas phase, SMxGAUSS also has Gaussian formatted input files and can = =3D > parse Gaussian output to run independently.

class=3D3D"khtml-block-placeholder">
Full details on the variou= s =3D > software packages (all of which are free) can be found at

class=3D3D"khtml-block-placeholder">
href=3D3D"http://comp.chem.umn.edu/smxgauss/"> > http://comp.chem.umn.edu/smxga=3D > uss/
href=3D3D"http://comp.chem.umn.edu/hondoplus/"> > http://comp.chem.umn.edu/hond=3D > oplus/
href=3D3D"http://comp.chem.umn.edu/gamessplus/"> > http://comp.chem.umn.edu/gam=3D > essplus/

class=3D3D"khtml-block-placeholder">
Best regards,
class=3D3D"khtml-block-placeholder">
Chris

class=3D3D"khtml-block-placeholder">
On Jan 9, 2006, at 9:18 AM= , =3D > Jianing Li jianing810[#]gmail.com wrote:

class=3D3D"Apple-interchange-newline">
style=3D3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =3D > margin-left: 0px; ">Sent to CCL by: "Jianing class=3D3D"Apple-converted-space">=3DA0 Li" [jianing810 _ =3D > gmail.com]
margin-bottom: 0px; margin-left: 0px; ">Dear All,
style=3D3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =3D > margin-left: 0px; ">I have a question about the geometry optimization in = =3D > solutions. I am eager to know a reliable and effective method to deal =3D > with the solution-phase optimization. I am using Gaussian03 but the =3D > difference in geometry is not as significant as we guess when comparing = =3D > the optimization in solution-phase and in gas-phase. What's more, there = =3D > are two problems of solution-phase optimization:
style=3D3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =3D > margin-left: 0px; ">1) It is very time-consuming to pursue optimization = =3D > in solutions.=3DA0
style=3D3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =3D > margin-left: 0px; ">2) It is hard to obtain the convergence. I am always = =3D > frustrated to find the unconvergence after several days' optimizing. And = =3D > during those convergent geometries, there are always small imaginary =3D > frequencies.
margin-bottom: 0px; margin-left: 0px; min-height: 14px; ">
style=3D3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =3D > margin-left: 0px; ">I know it is very controversial about the necessity = =3D > of solution-phase optimization, and I am wondering whether there is any = =3D > solution to solve this problem. Does anyone know the related software or = =3D > any tricks to do it in Gaussian?
margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: =3D > 14px; ">
margin-bottom: 0px; margin-left: 0px; ">Thanks a lot.
style=3D3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =3D > margin-left: 0px; min-height: 14px; ">
=3D > 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; =3D > ">Sincerely yours,
0px; margin-bottom: 0px; margin-left: 0px; ">Jianing
style=3D3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =3D > margin-left: 0px; min-height: 14px; ">
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margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: =3D > 14px; ">
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style=3D3D"margin: 0.0px 0.0px 0.0px 0.0px"> size=3D3D"3" style=3D3D"font: 12.0px Helvetica">--

style=3D3D"margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica; =3D > min-height: 14.0px">

0.0px"> Helvetica">Christopher J. Cramer

0.0px 0.0px 0.0px"> 12.0px Helvetica">University of Minnesota

0.0px 0.0px 0.0px 0.0px"> style=3D3D"font: 12.0px Helvetica">Department of Chemistry

style=3D3D"margin: 0.0px 0.0px 0.0px 0.0px"> size=3D3D"3" style=3D3D"font: 12.0px Helvetica">207 Pleasant St. =3D > SE

face=3D3D"Helvetica" size=3D3D"3" style=3D3D"font: 12.0px =3D > Helvetica">Minneapolis, MN 55455-0431

0.0px 0.0px 0.0px 0.0px"> style=3D3D"font: 12.0px Helvetica">--------------------------

= =3D >

size=3D3D"3" style=3D3D"font: 12.0px Helvetica">Phone: class=3D3D"Apple-converted-space">=3DA0 (612) 624-0859 || FAX: class=3D3D"Apple-converted-space">=3DA0 (612) 626-2006

=

style=3D3D"margin: 0.0px 0.0px 0.0px 0.0px"> size=3D3D"3" style=3D3D"font: 12.0px Helvetica">Mobile: (952) =3D > 297-2575

face=3D3D"Helvetica" size=3D3D"3" style=3D3D"font: 12.0px Helvetica"> href=3D3D"mailto:cramer| > ,|pollux.chem.umn.edu">cramer|,|pollux.chem.umn.edu<=3D > /FONT>

face=3D3D"Helvetica" size=3D3D"3" style=3D3D"font: 12.0px Helvetica"> href=3D3D"http://pollux.chem.umn.edu/~cramer"> > http://pollux.chem.umn.edu/~cr=3D > amer

face=3D3D"Helvetica" size=3D3D"3" style=3D3D"font: 12.0px Helvetica">(web= site =3D > includes information about the textbook "Essentials

style=3D3D"margin: 0.0px 0.0px 0.0px 0.0px"> size=3D3D"3" style=3D3D"font: 12.0px Helvetica"> class=3D3D"Apple-converted-space">=3DA0 =3DA0 of Computational =3D > Chemistry:=3DA0 Theories a= nd =3D > Models, 2nd Edition")


=3D > > --Apple-Mail-5--396687927-- > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > > ------=_Part_64385_27539802.1136883363883 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
Hi Chris,
Thank you for your answer - I've been having trouble getting my optimi= zations to converge using the PCM model in Gaussian03 too. I would like to = use SMxGAUSS with Gaussian03 output files of the converged gas phase calcul= ations. I looked at the link but I did not understand which platforms this = program works with. I prefer Windows but if it's impossible, I can use Linu= x (not Red Hat - some other less common distribution), or a G4 Ma= c with system 9 & 10 operating systems. Will any of these platforms wor= k with this program?
 
Thanks,
Avital

 
On 1/9/06, C= hristopher Cramer cramer . chem.umn.edu= <owner-chemistry(-)ccl.net= > wrote:
Sent to CCL by: Christopher Cram= er [cramer*o*chem.umn.edu]

--App= le-Mail-5--396687927
Content-Transfer-Encoding: 7bit
Content-Type: text/plain;
 &= nbsp;     charset=3DUS-ASCII;
   &nbs= p;   delsp=3Dyes;
       format= =3Dflowed

Jianing,

The SMx solvation models have nice, stable= gradients and optimize
efficiently. For instance, Christopher Hadad noted in a JACS paper afew years back that he found optimization of sugar geometries
impossibl= e with other solvation models but had no problem with SMx.

While we = are still waiting for G03 to make SMx models available (and
by waiting I don't mean that I expect it to happen anytime soon), themodels are available in HONDOPLUS, GAMESSPLUS, and SMxGAUSS. The
latte= r program is of particular use to Gaussian 03 users as it can be
invoked= with the Gaussian "external" keyword. For those with already
generated output files from the gas phase, SMxGAUSS also has Gaussianformatted input files and can parse Gaussian output to run
independent= ly.

Full details on the various software packages (all of which are = free)
can be found at

h= ttp://comp.chem.umn.edu/smxgauss/
http://comp.chem.umn.edu/hondoplus/
http://comp.chem.umn.edu/gamessplus/

Best regards,

Chris<= br>
On Jan 9, 2006, at 9:18 AM, Jianing Li jianing810[#]gmail.com wrote:=

> Sent to CCL by: "Jianing  Li" [jianing810 = _ gmail.com]
> Dear All,
> I have a question about the geomet= ry optimization in solutions. I
> am eager to know a reliable and eff= ective method to deal with the
> solution-phase optimization. I am us= ing Gaussian03 but the
> difference in geometry is not as significant as we guess when
&= gt; comparing the optimization in solution-phase and in gas-phase.
> = What's more, there are two problems of solution-phase optimization:
> 1) It is very time-consuming to pursue optimization in solutions.
&= gt; 2) It is hard to obtain the convergence. I am always frustrated to
&= gt; find the unconvergence after several days' optimizing. And during
> those convergent geometries, there are always small imaginary
> = frequencies.
>
> I know it is very controversial about the nece= ssity of solution-
> phase optimization, and I am wondering whether t= here is any
> solution to solve this problem. Does anyone know the related
&g= t; software or any tricks to do it in Gaussian?
>
> Thanks a lo= t.
>
> Sincerely yours,
> Jianing
>
>
>
> -=3D This is automatically added to each message by the mailin= g
> script =3D-
> To recover the email address of the author of= the message, please
> change>
> Search Messages: http://www.ccl.net/htdig  (login: ccl, Password:
> sear= ch)>
> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-= +-+-+-+-
> +-+-+
>
>
>

--

Christopher= J. Cramer
University of Minnesota
Department of Chemistry
207 Pleasant St. = SE
Minneapolis, MN 55455-0431
--------------------------
Phone:&nb= sp; (612) 624-0859 || FAX:  (612) 626-2006
Mobile: (952) = 297-2575
cramer|,|pollux.chem.umn.edu
http://pollux.chem.umn.e= du/~cramer
(website includes information about the textbook "Es= sentials
    of Computational Chemistry:  = Theories and Models, 2nd Edition")


--Apple-Mail-5--396687927
Content-Transfer-Encoding: quoted-= printable
Content-Type: text/html;
     &nbs= p; charset=3DISO-8859-1

<HTML><BODY style=3D3D"word-wr= ap: break-word; -khtml-nbsp-mode: space; =3D
-khtml-line-break: after-white-space; ">Jianing,<DIV><= BR =3D
class=3D3D"khtml-block-placeholder"></DIV><= DIV>The SMx solvation models =3D
have nice, stable gradients and opti= mize efficiently. For instance, =3D
Christopher Hadad noted in a JACS paper a few years back that he found = =3D
optimization of sugar geometries impossible with other solvation mod= els =3D
but had no problem with SMx.<DIV><BR =3D
class=3D3D&= quot;khtml-block-placeholder"></DIV><DIV>While we are s= till waiting =3D
for G03 to make SMx models available (and by waiting I don't mean that = I =3D
expect it to happen anytime soon), the models are available in =3D=
HONDOPLUS, GAMESSPLUS, and SMxGAUSS. The latter program is of particula= r =3D
use to Gaussian 03 users as it can be invoked with the Gaussian =3D
= "external" keyword. For those with already generated output files= from =3D
the gas phase, SMxGAUSS also has Gaussian formatted input file= s and can =3D
parse Gaussian output to run independently.</DIV><DIV><B= R =3D
class=3D3D"khtml-block-placeholder"></DIV><D= IV>Full details on the various =3D
software packages (all of which ar= e free) can be found at</DIV><DIV><BR =3D
class=3D3D"khtml-block-placeholder"></DIV><DIV>= ;<A =3D
href=3D3D"http://comp.chem.umn.edu/smxgauss/"> http://comp.chem.umn.edu/smxga=3D
uss/</A></DIV><DIV&= gt;<A =3D
href=3D3D"http://comp.chem.umn.edu/hondoplus/"> http://comp.chem.umn.edu/hond=3D
oplus/</A></DIV><DIV= ><A =3D
href=3D3D"http://comp.chem.umn.edu/gamessplus/"> http://comp.chem.umn.edu/gam=3D
essplus/</A></DIV><DI= V><BR =3D
class=3D3D"khtml-block-placeholder"></DI= V><DIV>Best regards,</DIV><DIV><BR =3D
class=3D3= D"khtml-block-placeholder"></DIV><DIV>Chris</DI= V><DIV><BR =3D
class=3D3D"khtml-block-placeholder"></DIV><DIV>= ;On Jan 9, 2006, at 9:18 AM, =3D
Jianing Li jianing810[#]gmail.com wrote= :<DIV><BR =3D
class=3D3D"Apple-interchange-newline"&g= t;<BLOCKQUOTE type=3D3D"cite"><DIV =3D
style=3D3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px;= =3D
margin-left: 0px; ">Sent to CCL by: "Jianing<SPAN = =3D
class=3D3D"Apple-converted-space">=3DA0 </SPAN>Li= " [jianing810 _ =3D
gmail.com]</DIV><DIV style=3D= 3D"margin-top: 0px; margin-right: 0px; =3D
margin-bottom: 0px; marg= in-left: 0px; ">Dear All,</DIV><DIV =3D
style=3D3D"= ;margin-top: 0px; margin-right: 0px; margin-bottom: 0px; =3D
margin-left: 0px; ">I have a question about the geometry optimi= zation in =3D
solutions. I am eager to know a reliable and effective met= hod to deal =3D
with the solution-phase optimization. I am using Gaussia= n03 but the =3D
difference in geometry is not as significant as we guess when comparing= =3D
the optimization in solution-phase and in gas-phase. What's more, t= here =3D
are two problems of solution-phase optimization:</DIV><= ;DIV =3D
style=3D3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px;= =3D
margin-left: 0px; ">1) It is very time-consuming to pursue = optimization =3D
in solutions.<SPAN class=3D3D"Apple-converted-s= pace">=3DA0</SPAN></DIV><DIV =3D
style=3D3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px;= =3D
margin-left: 0px; ">2) It is hard to obtain the convergence= . I am always =3D
frustrated to find the unconvergence after several day= s' optimizing. And =3D
during those convergent geometries, there are always small imaginary = =3D
frequencies.</DIV><DIV style=3D3D"margin-top: 0px; mar= gin-right: 0px; =3D
margin-bottom: 0px; margin-left: 0px; min-height: 14= px; "><BR></DIV><DIV =3D
style=3D3D"margin-top: 0px; margin-right: 0px; margin-bottom: 0px;= =3D
margin-left: 0px; ">I know it is very controversial about t= he necessity =3D
of solution-phase optimization, and I am wondering whet= her there is any =3D
solution to solve this problem. Does anyone know the related software o= r =3D
any tricks to do it in Gaussian?</DIV><DIV style=3D3D&quo= t;margin-top: 0px; =3D
margin-right: 0px; margin-bottom: 0px; margin-lef= t: 0px; min-height: =3D
14px; "><BR></DIV><DIV style=3D3D"margin-to= p: 0px; margin-right: 0px; =3D
margin-bottom: 0px; margin-left: 0px; &qu= ot;>Thanks a lot.</DIV><DIV =3D
style=3D3D"margin-top: = 0px; margin-right: 0px; margin-bottom: 0px; =3D
margin-left: 0px; min-height: 14px; "><BR></DIV><= ;DIV style=3D3D"margin-top: =3D
0px; margin-right: 0px; margin-bott= om: 0px; margin-left: 0px; =3D
">Sincerely yours,</DIV><= ;DIV style=3D3D"margin-top: 0px; margin-right: =3D
0px; margin-bottom: 0px; margin-left: 0px; ">Jianing</DIV>= ;<DIV =3D
style=3D3D"margin-top: 0px; margin-right: 0px; margin-= bottom: 0px; =3D
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------=_Part_64385_27539802.1136883363883-- From owner-chemistry@ccl.net Tue Jan 10 16:12:01 2006 From: "Daniel R McMasters daniel_mcmasters_+_merck.com" To: CCL Subject: CCL: Call for papers: ACS Fall 2006, ADME and Physical Property Prediction Message-Id: <-30453-060110152419-1701-Gm9TXRY9fCMIhXZ//7tUjg^server.ccl.net> X-Original-From: "Daniel R McMasters" Sent to CCL by: "Daniel R McMasters" [daniel_mcmasters_-_merck.com] 1st Call for papers ADME and Physical Property Prediction Symposium 232nd ACS National Meeting San Francisco, Sept. 10-14, 2006 COMP division ============================================================ Dear Colleagues, You are invited to submit contributions for this symposium focusing on the development or application of computational models for ADMET and physical property prediction. Relevant topics include (but are not limited to): P450 metabolism, inhibition and induction; permeability and absorption phenomena (bioavailability, CNS penetration); toxicity; plasma protein binding; solubility and logD. We are striving for a mixture of contributions from academic laboratories, pharmaceutical and chemical industries, and computational chemistry software companies. Please use the on-line abstract submission system (OASYS) for submitting your abstract (http://oasys.acs.org/oasys.htm). OASYS will be accepting abstracts between February 20 and April 25, 2006. This symposium is being organized by Daniel McMasters and Matt Walker of Merck Research Laboratories, Rahway, NJ. Please contact either of us with any questions. Thanks, and we look forward to your submission! Daniel R. McMasters, Ph.D. Senior Research Chemist Merck & Co., Inc. RY50SW-100 P.O.Box 2000 Rahway, NJ 07065-0900 Tel: (732) 594-6812 Fax: (732) 594-4224 email: daniel_mcmasters[a]merck.com Matthew J. Walker, Ph.D. Research Fellow Merck & Co., Inc. RY50SW-100 P.O. Box 2000, Rahway NJ 07065-0900 Tel: (732) 594-8575 Fax: (732) 594-4224 email: matthew_walker[a]merck.com