From owner-chemistry@ccl.net Mon Mar 15 01:41:00 2010 From: "Alfredo Tlahuice tlahuicef{:}yahoo.com" To: CCL Subject: CCL: How to calculate Au32 on G03 Message-Id: <-41435-100314225831-26723-UNCu3teik5eooyGJba7PJg[]server.ccl.net> X-Original-From: "Alfredo Tlahuice" Date: Sun, 14 Mar 2010 22:58:27 -0400 Sent to CCL by: "Alfredo Tlahuice" [tlahuicef- -yahoo.com] Hello there. I am trying to calculate de IR spectrum of the Au32 with a Ih symmetry, but after a lot of time, the output file shows an error. The error message is: Density matrix breaks symmetry, PCut= 1.00D-04 Density has only Abelian symmetry. I have read that the reason is on the SCF cycle, but I have not idea how to overcome this. The keywords I have been using are: Int(Grid=99590) SCF(IntRep,NoVarAcc,Tight) Moreover the LAND2DZ basis is used in this calculation. Does anybody have an advice? From owner-chemistry@ccl.net Mon Mar 15 13:23:00 2010 From: "Lochana C Menikarachchi lochanac^^yahoo.com" To: CCL Subject: CCL: Water molecules participating in Enzymatic Reactions Message-Id: <-41436-100315132041-12284-tx7+fiNAb1ZSnegnnj7hZA,+,server.ccl.net> X-Original-From: "Lochana C Menikarachchi" Date: Mon, 15 Mar 2010 13:20:37 -0400 Sent to CCL by: "Lochana C Menikarachchi" [lochanac#,#yahoo.com] Dear All, I need to model an enzymatic reaction in which explicit water molecules participate in some steps. For example hydrolysis steps. I am going to estimate QM/MM reaction and activation energy barriers for all the steps involved. Problem is how do i include the waters for some steps in the middle of the reaction profile. I am going to use several MD snapshot as starting structures, but will be striping off waters. What about doing an MD simulation with water for the particular structure and select some waters around the active site. In that case the problem is how many? just one..may be couple of more waters bound to the particular water molecule involved?? Several shells of water..Can anyone help me to find journal articles on similar problems. Any citations or suggestions are mostly welcomed. Thank you all in advance. LC From owner-chemistry@ccl.net Mon Mar 15 13:58:00 2010 From: "Jamin Krinsky jamink-*-berkeley.edu" To: CCL Subject: CCL:G: help Message-Id: <-41437-100315131329-11821-01r4I3zX0/6dVmfZMUfiFQ]![server.ccl.net> X-Original-From: Jamin Krinsky Content-Type: multipart/alternative; boundary=0016e64d94a4f060300481d925b2 Date: Mon, 15 Mar 2010 09:12:31 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink/a\berkeley.edu] --0016e64d94a4f060300481d925b2 Content-Type: text/plain; charset=ISO-8859-1 Hi Emran, If it is not dying until link502 (SCF) than it's more than just a syntax problem. The SCIPCM model can cause SCF convergence difficulties (you should list the exact error message in your post). One work-around might be to make sure it converges in the gas phase then use that as an initial guess, although the program might more or less do that for you, I can't remember. Consider using the normal PCM model, which is obviously non-self-consistent but generally works well and doesn't have the convergence problems. Regards, Jamin On Sat, Mar 13, 2010 at 1:53 PM, zoran matovic zmatovic,+,kg.ac.rs < owner-chemistry]-[ccl.net> wrote: > Emran, > there is no "sci-pcm" option but just "scipcm" > So try scrf=(scipcm, solvent=water) > > zoran > > ----- Original Message ----- > *From:* Emran Heshmati heshmaty{:}yahoo.com > *To:* Matovic, Zoran D > *Sent:* Saturday, March 13, 2010 12:51 PM > *Subject:* CCL:G: help > > Hi all > I wanna to perform DFT calculation on a smal peptide in water solution > using GAUSSIAN 03. I use this keyword in the "route section": # > b3lyp/6-31g* fopt freq=noraman scrf=(sci-pcm, solvent=water) . but it > don't work (error l502.exe ). can anyone help me? > ** > *Best Regards > Emran Heshmati > *P *Save a tree... please don't print this e-mail unless you really need > to* > > ------------------------------ > Get your preferred Email name! > > Now you can [#]ymail.com and [#]rocketmail.com. > > ------------------------------ > > > No virus found in this incoming message. > Checked by AVG - www.avg.com > Version: 9.0.733 / Virus Database: 271.1.1/2743 - Release Date: 03/13/10 > 08:33:00 > > -- Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink]-[berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu --0016e64d94a4f060300481d925b2 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Emran,
If it is not dying until link502 (SCF) than it's more than= just a syntax problem. The SCIPCM model can cause SCF convergence difficul= ties (you should list the exact error message in your post). One work-aroun= d might be to make sure it converges in the gas phase then use that as an i= nitial guess, although the program might more or less do that for you, I ca= n't remember. Consider using the normal PCM model, which is obviously n= on-self-consistent but generally works well and doesn't have the conver= gence problems.
Regards,
Jamin


On Sat, Mar 13, 201= 0 at 1:53 PM, zoran matovic zmatovic,+,kg.ac.rs= <owner= -chemistry]-[ccl.net> wrote:
Emran,
there is no "sci-pcm" option= but just=20 "scipcm"
So try=A0 scrf=3D(scipcm,=20 solvent=3Dwater)
=A0
zoran
----- Original Message -----
To: Matovic, Zoran D
Sent: Saturday, March 13, 2010 12= :51=20 PM
Subject: CCL:G: help

Hi all
I wanna to perform DFT calculation on a smal peptide in water= =20 solution using GAUSSIAN 03. I use this keyword in the "route s= ection":=20 # b3lyp/6-31g* fopt freq=3Dnoraman scrf=3D(= sci-pcm,=20 solvent=3Dwater) . but it don't work (error l502.exe=A0)= . can=20 anyone help me?
=A0
Best Regard= s
Emran=20 Heshmati
P=20 Save a=20 tree... please don't print this e-mail unless you really need= =20 to

Get=20 your preferred Email name!
Now you can [#]ymail.com and=20 [#]rocketmail.com= .


No virus found in this incoming message.
Checked by AVG -= =20 www.avg.com
Vers= ion: 9.0.733 / Virus Database: 271.1.1/2743 - Release=20 Date: 03/13/10 08:33:00



--
Jamin L Krinsky, Ph.D.<= br>Molecular Graphics and Computation Facility
175 Tan Hall, University = of California, Berkeley, CA 94720
jamink]-[berkeley.edu, 510-643-0616
http://glab.cchem.berkeley.edu

--0016e64d94a4f060300481d925b2-- From owner-chemistry@ccl.net Mon Mar 15 15:41:00 2010 From: "Senthil Natesan sen.natesan]^[yahoo.com" To: CCL Subject: CCL: Essential books in computational chemistry (drug design) Message-Id: <-41438-100315153543-963-azeqOzV7TzBnxumDlm5wGA[]server.ccl.net> X-Original-From: "Senthil Natesan" Date: Mon, 15 Mar 2010 15:35:39 -0400 Sent to CCL by: "Senthil Natesan" [sen.natesan,yahoo.com] Dear All, Greetings. It will be very helpful if you could recommend a few essential (authoritative in its area) books in the following areas 1) Molecular dynamics simulation 2) Molecular recognition 3) QM/MM calculations 4) QSAR 5) ADMET Books published after 2000 would be great as it would cover the latest developments. Thanks everyone for your time and valuable recommendations. Senthil Natesan, From owner-chemistry@ccl.net Mon Mar 15 17:06:00 2010 From: "Jamin Krinsky jamink_._berkeley.edu" To: CCL Subject: CCL:G: How to calculate Au32 on G03 Message-Id: <-41439-100315170412-20342-CM+jN/Zc8FaWSvYSsaUUrg(0)server.ccl.net> X-Original-From: Jamin Krinsky Content-Type: multipart/alternative; boundary=0016363b83a40653a70481dd3890 Date: Mon, 15 Mar 2010 14:03:54 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink+/-berkeley.edu] --0016363b83a40653a70481dd3890 Content-Type: text/plain; charset=ISO-8859-1 Hi Alfredo, G03 only uses Abelian symmetry, for instance if you use automatic symmetry with a C3V structure it will only use Cs and give you that error message. However, the calculation should still run, just in that lower symmetry. Are you getting SCF convergence failures? If so try playing with level shifting and maybe quadratic convergence (QC or XQC). Regards, Jamin On Sun, Mar 14, 2010 at 7:58 PM, Alfredo Tlahuice tlahuicef{:}yahoo.com < owner-chemistry_._ccl.net> wrote: > > Sent to CCL by: "Alfredo Tlahuice" [tlahuicef- -yahoo.com] > Hello there. > I am trying to calculate de IR spectrum of the Au32 with a Ih symmetry, but > after a lot of time, the output file shows an error. > > The error message is: > Density matrix breaks symmetry, PCut= 1.00D-04 > Density has only Abelian symmetry. > > I have read that the reason is on the SCF cycle, but I have not idea how to > overcome this. > > The keywords I have been using are: > Int(Grid=99590) SCF(IntRep,NoVarAcc,Tight) > > Moreover the LAND2DZ basis is used in this calculation. > > Does anybody have an advice?> > > -- Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink_._berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu --0016363b83a40653a70481dd3890 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Alfredo,
G03 only uses Abelian symmetry, for instance if you use=20 automatic symmetry with a C3V structure it will only use Cs and give you that error message. However, the calculation should still run, just in=20 that lower symmetry. Are you getting SCF convergence failures? If so try playing with level shifting and maybe quadratic convergence (QC or=20 XQC).
Regards,
Jamin

On Sun, Mar 14, 2010 at= 7:58 PM, Alfredo Tlahuice tlahuicef{:}yahoo.c= om <own= er-chemistry_._ccl.net> wrote:

Sent to CCL by: "Alfredo =A0Tlahuice" [tlahuicef- -yahoo.com]
Hello there.
I am trying to calculate de IR spectrum of the Au32 with a Ih symmetry, but= after a lot of time, the output file shows an error.

The error message is:
Density matrix breaks symmetry, PCut=3D 1.00D-04
=A0Density has only Abelian symmetry.

I have read that the reason is on the SCF cycle, but I have not idea how to= overcome this.

The keywords I have been using are:
Int(Grid=3D99590) SCF(IntRep,NoVarAcc,Tight)

Moreover the LAND2DZ basis is used in this calculation.

Does anybody have an advice?



-=3D This is automatically added to each message by the mailing script =3D-=
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--
Jamin L Krinsky, Ph.D.<= br>Molecular Graphics and Computation Facility
175 Tan Hall, University = of California, Berkeley, CA 94720
jamink_._berkeley.edu, 510-643-0616
http://glab.cchem.berkeley.edu

--0016363b83a40653a70481dd3890-- From owner-chemistry@ccl.net Mon Mar 15 17:40:00 2010 From: "Barbault Florent florent.barbault*_*univ-paris-diderot.fr" To: CCL Subject: CCL: Essential books in computational chemistry (drug design) Message-Id: <-41440-100315165621-19526-v6lGafrV6RatJ+nivftnTA]*[server.ccl.net> X-Original-From: "Barbault Florent" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="ISO-8859-1"; format="flowed" Date: Mon, 15 Mar 2010 21:56:08 +0100 MIME-Version: 1.0 Sent to CCL by: "Barbault Florent" [florent.barbault/./univ-paris-diderot.fr] Hi, Personnaly, I found the book "molecular modelling: principles and applications" very useful... Here is the link on amazon (I have no interest on this book!) http://www.amazon.com/Molecular-Modelling-Principles-Applications-2nd/dp/0582382106/ref=sr_1_1?ie=UTF8&s=books&qid=1268686522&sr=8-1 Best regards Florent Barbault On Mon, 15 Mar 2010 15:35:39 -0400 "Senthil Natesan sen.natesan]^[yahoo.com" wrote: > > Sent to CCL by: "Senthil Natesan" [sen.natesan,yahoo.com] > Dear All, > > Greetings. It will be very helpful if you could recommend a few >essential (authoritative in its area) books in the following areas > > 1) Molecular dynamics simulation > 2) Molecular recognition > 3) QM/MM calculations > 4) QSAR > 5) ADMET > > Books published after 2000 would be great as it would cover the >latest developments. > > Thanks everyone for your time and valuable recommendations. > > Senthil Natesan, > > > > -= This is automatically added to each message by the mailing script >=- > To recover the email address of the author of the message, please >change> Conferences: >http://server.ccl.net/chemistry/announcements/conferences/> > ------------------------------------------------- Dr Florent Barbault Maitre de conferences / Assistant professor Universite Paris Diderot Laboratoire ITODYS 15 rue Jean de Baïf, bâtiment Lavoisier 75013 Paris FRANCE http://www.itodys.univ-paris7.fr/ tel : (33) 01-57-27-88-50 e-mail : florent.barbault(~)univ-paris-diderot.fr ------------------------------------------------- From owner-chemistry@ccl.net Mon Mar 15 19:31:00 2010 From: "Cyril Bauvais cyril.bauvais^u-psud.fr" To: CCL Subject: CCL: Essential books in computational chemistry (drug design) Message-Id: <-41441-100315192916-19680-K//0jVkEH0dI70caoSPBiQ_-_server.ccl.net> X-Original-From: Cyril Bauvais Content-Type: multipart/alternative; boundary=001485f7cbee2a3d190481df3fd1 Date: Tue, 16 Mar 2010 00:29:04 +0100 MIME-Version: 1.0 Sent to CCL by: Cyril Bauvais [cyril.bauvais/a\u-psud.fr] --001485f7cbee2a3d190481df3fd1 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Senthil, Salut Florent this one is also very good : Molecular Modeling of Inorganic Compounds, 3rd Edition Peter Comba, Trevor W. Hambley, Bodo Martin ISBN: 978-3-527-31799-8 http://eu.wiley.com/WileyCDA/WileyTitle/productCd-3527317996,descCd-tableOf= Contents.html About ADME, recent review articles should give you up to date informations about it... Best, Cyril 2010/3/15 Barbault Florent florent.barbault*_*univ-paris-diderot.fr < owner-chemistry- -ccl.net> > > Sent to CCL by: "Barbault Florent" [florent.barbault/./ > univ-paris-diderot.fr] > Hi, > > Personnaly, I found the book "molecular modelling: principles and > applications" very useful... Here is the link on amazon (I have no intere= st > on this book!) > > > http://www.amazon.com/Molecular-Modelling-Principles-Applications-2nd/dp/= 0582382106/ref=3Dsr_1_1?ie=3DUTF8&s=3Dbooks&qid=3D1268686522&sr=3D8-1 > > Best regards > Florent Barbault > > > > On Mon, 15 Mar 2010 15:35:39 -0400 > "Senthil Natesan sen.natesan]^[yahoo.com" > wrote: > >> >> Sent to CCL by: "Senthil Natesan" [sen.natesan,yahoo.com] >> Dear All, >> >> Greetings. It will be very helpful if you could recommend a few essenti= al >> (authoritative in its area) books in the following areas >> >> 1) Molecular dynamics simulation >> 2) Molecular recognition >> 3) QM/MM calculations >> 4) QSAR >> 5) ADMET >> >> Books published after 2000 would be great as it would cover the latest >> developments. >> >> Thanks everyone for your time and valuable recommendations. >> >> Senthil Natesan, >> >> >> >> -=3D This is automatically added to each message by the mailing script = =3D-=> >> > > ------------------------------------------------- > Dr Florent Barbault > Maitre de conferences / Assistant professor > > Universite Paris Diderot > Laboratoire ITODYS > 15 rue Jean de Ba=C4=BCf, b=C4=81timent Lavoisier > 75013 Paris FRANCE > http://www.itodys.univ-paris7.fr/ > tel : (33) 01-57-27-88-50 > e-mail : florent.barbault=3Duniv-paris-diderot.fr > ------------------------------------------------- > > > > > -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --001485f7cbee2a3d190481df3fd1 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Senthil, Salut Florent

this one is also very good :
Molecular Modeling of Inorganic Compounds, 3rd E= dition
Peter Comba, Trevor W. Hambley, Bodo Martin
ISBN: 978-3-527-31799-8
http://eu.wiley.com/WileyCDA/WileyTitle/productCd-352731= 7996,descCd-tableOfContents.html

About ADME, recent review articles should give you up to date informati= ons about it...

Best,

Cyril




2010/3/15 Barbault Florent florent.barbault*_*univ-paris-diderot.fr <owner-chemistry- -ccl.ne= t>

Sent to CCL by: "Barbault Florent" [florent.barbault/./univ-paris-diderot.fr]=
Hi,

Personnaly, I found the book "molecular modelling: principles and appl= ications" very useful... Here is the link on amazon (I have no interes= t on this book!)

http://www.amazon.com/Molecular-Modellin= g-Principles-Applications-2nd/dp/0582382106/ref=3Dsr_1_1?ie=3DUTF8&s=3D= books&qid=3D1268686522&sr=3D8-1

Best regards
Florent Barbault



On Mon, 15 Mar 2010 15:35:39 -0400
=C2=A0"Senthil Natesan sen.natesan]^[yahoo.com" <owner-chemistry=3Dccl.net> wrote:

Sent to CCL by: "Senthil =C2=A0 Natesan" [sen.natesan,yahoo.com]
Dear All,

Greetings. It will be very helpful =C2=A0if you could recommend a few essen= tial (authoritative in its area) books in the following areas

1) Molecular dynamics simulation
2) Molecular recognition
3) QM/MM calculations
4) QSAR
5) ADMET

Books published after 2000 would be great as it would cover the latest deve= lopments.

Thanks everyone for your time and valuable recommendations.

Senthil Natesan,



-=3D This is automatically added to each message by the mailing script =3D-=
http://server.ccl.net/chemistry/announcements/= conferences/>

-------------------------------------------------
Dr Florent Barbault
Maitre de conferences / Assistant professor

Universite Paris Diderot
Laboratoire ITODYS
15 rue Jean de Ba=C4=BCf, b=C4=81timent Lavoisier
75013 Paris FRANCE
http://www.= itodys.univ-paris7.fr/
tel =C2=A0: (33) 01-57-27-88-50
e-mail : florent.barbault=3Duniv-paris-diderot.fr
-------------------------------------------------




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

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--001485f7cbee2a3d190481df3fd1-- From owner-chemistry@ccl.net Mon Mar 15 22:53:01 2010 From: "Yvonne Martin yvonnecmartin_+_gmail.com" To: CCL Subject: CCL: Essential books in computational chemistry (drug design) Message-Id: <-41442-100315221343-27691-OdixjIiI30XsIYGC4FyTvg%x%server.ccl.net> X-Original-From: Yvonne Martin Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=UTF-8 Date: Mon, 15 Mar 2010 20:42:11 -0500 MIME-Version: 1.0 Sent to CCL by: Yvonne Martin [yvonnecmartin\a/gmail.com] The second edition of my book "Quantitative Drug Design" is in press. I don't have a publication date, but the publisher indicates April or May. Yvonne Martin On Mon, Mar 15, 2010 at 6:29 PM, Cyril Bauvais cyril.bauvais^u-psud.fr wrote: > Hi Senthil, Salut Florent > > this one is also very good : > Molecular Modeling of Inorganic Compounds, 3rd Edition > Peter Comba, Trevor W. Hambley, Bodo Martin > ISBN: 978-3-527-31799-8 > http://eu.wiley.com/WileyCDA/WileyTitle/productCd-3527317996,descCd-table= OfContents.html > > About ADME, recent review articles should give you up to date information= s > about it... > > Best, > > Cyril > > > > > 2010/3/15 Barbault Florent florent.barbault*_*univ-paris-diderot.fr > >> >> Sent to CCL by: "Barbault Florent" >> [florent.barbault/./univ-paris-diderot.fr] >> Hi, >> >> Personnaly, I found the book "molecular modelling: principles and >> applications" very useful... Here is the link on amazon (I have no inter= est >> on this book!) >> >> >> http://www.amazon.com/Molecular-Modelling-Principles-Applications-2nd/dp= /0582382106/ref=3Dsr_1_1?ie=3DUTF8&s=3Dbooks&qid=3D1268686522&sr=3D8-1 >> >> Best regards >> Florent Barbault >> >> >> On Mon, 15 Mar 2010 15:35:39 -0400 >> =C2=A0"Senthil Natesan sen.natesan]^[yahoo.com" >> wrote: >>> >>> Sent to CCL by: "Senthil =C2=A0 Natesan" [sen.natesan,yahoo.com] >>> Dear All, >>> >>> Greetings. It will be very helpful =C2=A0if you could recommend a few >>> essential (authoritative in its area) books in the following areas >>> >>> 1) Molecular dynamics simulation >>> 2) Molecular recognition >>> 3) QM/MM calculations >>> 4) QSAR >>> 5) ADMET >>> >>> Books published after 2000 would be great as it would cover the latest >>> developments. >>> >>> Thanks everyone for your time and valuable recommendations. >>> >>> Senthil Natesan, >>> >>> >>> >>> -=3D This is automatically added to each message by the mailing script = =3D- >>> http://server.ccl.net/chemistry/announcements/conferences/> >> >> ------------------------------------------------- >> Dr Florent Barbault >> Maitre de conferences / Assistant professor >> >> Universite Paris Diderot >> Laboratoire ITODYS >> 15 rue Jean de Ba=C4=BCf, b=C4=81timent Lavoisier >> 75013 Paris FRANCE >> http://www.itodys.univ-paris7.fr/ >> tel =C2=A0: (33) 01-57-27-88-50 >> e-mail : florent.barbault=3Duniv-paris-diderot.fr >> ------------------------------------------------- >> >> >> >> -=3D This is automatically added to each message by the mailing script = =3D- >> E-mail to subscribers: CHEMISTRY]*[ccl.net or use: >> =C2=A0 =C2=A0>> >> E-mail to administrators: CHEMISTRY-REQUEST]*[ccl.net or use >> =C2=A0 =C2=A0Conferences: >> http://server.ccl.net/chemistry/announcements/conferences/>> =C2=A0 =C2=A0>> >> > > From owner-chemistry@ccl.net Mon Mar 15 23:27:01 2010 From: "Xiaohui Kang huixiaokang328::163.com" To: CCL Subject: CCL: problem on g09 Message-Id: <-41443-100315211751-23398-/7FbA/XPK+YXQN80/Q18LA!=!server.ccl.net> X-Original-From: "Xiaohui Kang" Date: Mon, 15 Mar 2010 21:17:47 -0400 Sent to CCL by: "Xiaohui Kang" [huixiaokang328 ~~ 163.com] Dear CCL Subscribers When I compute the thermochemistry of water at both 298.15K and 373K in an input file with g09,I can not get the information on 373K ,that is to say,the "--Link--" does not play a role in my calculation.The following is my input file : %Chk=watertest.chk %nproc=8 #T RHF/6-31G(d) Freq=noraman water298 0 1 O 0.00000000 0.00000000 0.11980000 H 0.00000000 0.76140000 -0.47910000 H 0.00000000 -0.76140000 -0.47910000 --Link1-- %Chk=watertest.chk %nproc=8 #T RHF/6-31G(d) Geom=Check Freq=ReadFC Guess=Read Test water373 0 1 373.0 1.0 0.9 16 1 1 Can anybody tell me what is the reason resulting in this phenomenon? Sincerely xkang