From owner-chemistry@ccl.net Mon Mar 15 01:41:00 2010
From: "Alfredo Tlahuice tlahuicef{:}yahoo.com" <owner-chemistry[]server.ccl.net>
To: CCL
Subject: CCL: How to calculate Au32 on G03
Message-Id: <-41435-100314225831-26723-UNCu3teik5eooyGJba7PJg[]server.ccl.net>
X-Original-From: "Alfredo Tlahuice" <tlahuicef||yahoo.com>
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" <owner-chemistry,+,server.ccl.net>
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" <lochanac:-:yahoo.com>
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" <owner-chemistry]![server.ccl.net>
To: CCL
Subject: CCL:G: help
Message-Id: <-41437-100315131329-11821-01r4I3zX0/6dVmfZMUfiFQ]![server.ccl.net>
X-Original-From: Jamin Krinsky <jamink .. berkeley.edu>
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
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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 <owner-chemistry+%3A+ccl.net>
> *To:* Matovic, Zoran D <zmatovic+%3A+kg.ac.yu>
> *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!
> <http://sg.rd.yahoo.com/aa/mail/domainchoice/mail/signature/*http://mail.promotions.yahoo.com/newdomains/aa/>
> 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,<br>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.<br>
Regards,<br>Jamin<br><br><br><div class=3D"gmail_quote">On Sat, Mar 13, 201=
0 at 1:53 PM, zoran matovic zmatovic,+,<a href=3D"http://kg.ac.rs">kg.ac.rs=
</a> <span dir=3D"ltr"><<a href=3D"mailto:owner-chemistry]-[ccl.net">owner=
-chemistry]-[ccl.net</a>></span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin: 0pt 0pt 0pt 0.8ex; borde=
r-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div bgcolor=3D"#ffffff">
<div>
<div><font face=3D"Arial" size=3D"2">Emran,</font></div>
<div>
<div><font face=3D"Arial" size=3D"2">there is no "sci-pcm" option=
but just=20
"scipcm"</font></div>
<div><font face=3D"Arial" size=3D"2">So try=A0 scrf=3D(scipcm,=20
solvent=3Dwater)</font></div>
<div><font face=3D"Arial" size=3D"2"></font>=A0</div>
<div><font face=3D"Arial" size=3D"2">zoran</font></div></div></div>
<blockquote style=3D"border-left: 2px solid rgb(0, 0, 0); padding-left: 5px=
; padding-right: 0px; margin-left: 5px; margin-right: 0px;"><div><div></div=
><div class=3D"h5">
<div style=3D"font: 10pt arial;">----- Original Message ----- </div>
<div style=3D"font: 10pt arial; background: none repeat scroll 0% 0% rgb(=
228, 228, 228);"><b>From:</b>=20
<a title=3D"owner-chemistry" href=3D"mailto:owner-chemistry+%3A+ccl.net" =
target=3D"_blank">Emran=20
Heshmati heshmaty{:}yahoo.com</a> </div>
<div style=3D"font: 10pt arial;"><b>To:</b> <a title=3D"zmatovic" href=3D=
"mailto:zmatovic+%3A+kg.ac.yu" target=3D"_blank">Matovic, Zoran D </a> </di=
v>
<div style=3D"font: 10pt arial;"><b>Sent:</b> Saturday, March 13, 2010 12=
:51=20
PM</div>
<div style=3D"font: 10pt arial;"><b>Subject:</b> CCL:G: help</div>
<div><br></div>
<table border=3D"0" cellpadding=3D"0" cellspacing=3D"0">
<tbody>
<tr>
<td valign=3D"top">
<div>Hi all </div>
<div>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
<font color=3D"#ff0000"># b3lyp/6-31g* fopt freq=3Dnoraman scrf=3D(=
sci-pcm,=20
solvent=3Dwater) </font>. but it don't work (error l502.exe=A0)=
. can=20
anyone help me?<br></div>
<div><i><font color=3D"#00bf60"><font color=3D"#00bf60"></font></fo=
nt></i>=A0</div>
<div><i><font color=3D"#00bf60"><font color=3D"#00bf60">Best Regard=
s<br>Emran=20
Heshmati</font><br></font></i><span style=3D"font-family: Webdings;=
color: green; font-size: 18pt;">P=20
</span><span style=3D"color: green; font-size: 8pt;" lang=3D"EN-GB"=
><i>Save a=20
tree... please don't print this e-mail unless you really need=
=20
to</i></span></div></td></tr></tbody></table><br>
<hr size=3D"1">
<a href=3D"http://sg.rd.yahoo.com/aa/mail/domainchoice/mail/signature/*ht=
tp://mail.promotions.yahoo.com/newdomains/aa/" target=3D"_blank">Get=20
your preferred Email name! </a><br>Now you can [#]<a href=3D"http://ymail=
.com" target=3D"_blank">ymail.com</a> and=20
[#]<a href=3D"http://rocketmail.com" target=3D"_blank">rocketmail.com</a>=
.
</div></div><p>
</p><hr>
<p></p><br>No virus found in this incoming message.<br>Checked by AVG -=
=20
<a href=3D"http://www.avg.com" target=3D"_blank">www.avg.com</a> <br>Vers=
ion: 9.0.733 / Virus Database: 271.1.1/2743 - Release=20
Date: 03/13/10 08:33:00<br></blockquote></div>
</blockquote></div><br><br clear=3D"all"><br>-- <br>Jamin L Krinsky, Ph.D.<=
br>Molecular Graphics and Computation Facility<br>175 Tan Hall, University =
of California, Berkeley, CA 94720<br><a href=3D"mailto:jamink]-[berkeley.edu"=
>jamink]-[berkeley.edu</a>, 510-643-0616<br>
<a href=3D"http://glab.cchem.berkeley.edu">http://glab.cchem.berkeley.edu</=
a><br><br>
--0016e64d94a4f060300481d925b2--
From owner-chemistry@ccl.net Mon Mar 15 15:41:00 2010
From: "Senthil Natesan sen.natesan]^[yahoo.com" <owner-chemistry[]server.ccl.net>
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" <sen.natesan/./yahoo.com>
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" <owner-chemistry(0)server.ccl.net>
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 <jamink%x%berkeley.edu>
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,<br>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).<br>
Regards,<br>Jamin<br><br><div class=3D"gmail_quote">On Sun, Mar 14, 2010 at=
7:58 PM, Alfredo Tlahuice tlahuicef{:}<a href=3D"http://yahoo.com">yahoo.c=
om</a> <span dir=3D"ltr"><<a href=3D"mailto:owner-chemistry_._ccl.net">own=
er-chemistry_._ccl.net</a>></span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin: 0pt 0pt 0pt 0.8ex; borde=
r-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><br>
Sent to CCL by: "Alfredo =A0Tlahuice" [tlahuicef- -<a href=3D"htt=
p://yahoo.com" target=3D"_blank">yahoo.com</a>]<br>
Hello there.<br>
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.<br>
<br>
The error message is:<br>
Density matrix breaks symmetry, PCut=3D 1.00D-04<br>
=A0Density has only Abelian symmetry.<br>
<br>
I have read that the reason is on the SCF cycle, but I have not idea how to=
overcome this.<br>
<br>
The keywords I have been using are:<br>
Int(Grid=3D99590) SCF(IntRep,NoVarAcc,Tight)<br>
<br>
Moreover the LAND2DZ basis is used in this calculation.<br>
<br>
Does anybody have an advice?<br>
<br>
<br>
<br>
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<br>
</blockquote></div><br><br clear=3D"all"><br>-- <br>Jamin L Krinsky, Ph.D.<=
br>Molecular Graphics and Computation Facility<br>175 Tan Hall, University =
of California, Berkeley, CA 94720<br><a href=3D"mailto:jamink_._berkeley.edu"=
>jamink_._berkeley.edu</a>, 510-643-0616<br>
<a href=3D"http://glab.cchem.berkeley.edu">http://glab.cchem.berkeley.edu</=
a><br><br>
--0016363b83a40653a70481dd3890--
From owner-chemistry@ccl.net Mon Mar 15 17:40:00 2010
From: "Barbault Florent florent.barbault*_*univ-paris-diderot.fr" <owner-chemistry]*[server.ccl.net>
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" <florent.barbault a univ-paris-diderot.fr>
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" <owner-chemistry(~)ccl.net>
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 Ba�f, b�timent 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" <owner-chemistry_-_server.ccl.net>
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 <cyril.bauvais:u-psud.fr>
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
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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" <owner-chemistry=3Dccl.net>
> 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/>
>
>
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Content-Transfer-Encoding: quoted-printable
Hi Senthil, Salut Florent <br><br>this one is also very good : <br><div cla=
ss=3D"productDetail-title">Molecular Modeling of Inorganic Compounds, 3rd E=
dition</div>
<div class=3D"productDetail-biblio">
<div class=3D"productDetail-authors"><span class=3D"productDetail-authorsMa=
in">Peter Comba, Trevor W. Hambley, Bodo Martin</span> </div>
<div class=3D"productDetail-productCode">ISBN: 978-3-527-31799-8<br><a href=
=3D"http://eu.wiley.com/WileyCDA/WileyTitle/productCd-3527317996,descCd-tab=
leOfContents.html">http://eu.wiley.com/WileyCDA/WileyTitle/productCd-352731=
7996,descCd-tableOfContents.html</a><br>
<br>About ADME, recent review articles should give you up to date informati=
ons about it...<br><br>Best,<br><br>Cyril<br><br><br></div></div><br><br><d=
iv class=3D"gmail_quote">2010/3/15 Barbault Florent florent.barbault*_*<a h=
ref=3D"http://univ-paris-diderot.fr">univ-paris-diderot.fr</a> <span dir=3D=
"ltr"><<a href=3D"mailto:owner-chemistry- -ccl.net">owner-chemistry- -ccl.ne=
t</a>></span><br>
<blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid rgb(204, =
204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
Sent to CCL by: "Barbault Florent" [florent.barbault/./<a href=3D=
"http://univ-paris-diderot.fr" target=3D"_blank">univ-paris-diderot.fr</a>]=
<br>
Hi,<br>
<br>
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!)<br>
<br>
<a href=3D"http://www.amazon.com/Molecular-Modelling-Principles-Application=
s-2nd/dp/0582382106/ref=3Dsr_1_1?ie=3DUTF8&s=3Dbooks&qid=3D12686865=
22&sr=3D8-1" target=3D"_blank">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</a><br>
<br>
Best regards<br>
Florent Barbault<div class=3D"im"><br>
<br>
<br>
On Mon, 15 Mar 2010 15:35:39 -0400<br>
=C2=A0"Senthil Natesan sen.natesan]^[<a href=3D"http://yahoo.com" targ=
et=3D"_blank">yahoo.com</a>" <owner-chemistry=3D<a href=3D"http://c=
cl.net" target=3D"_blank">ccl.net</a>> wrote:<br>
</div><blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid rgb=
(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class=
=3D"im">
<br>
Sent to CCL by: "Senthil =C2=A0 Natesan" [sen.natesan,<a href=3D"=
http://yahoo.com" target=3D"_blank">yahoo.com</a>]<br>
Dear All,<br>
<br>
Greetings. It will be very helpful =C2=A0if you could recommend a few essen=
tial (authoritative in its area) books in the following areas<br>
<br>
1) Molecular dynamics simulation<br>
2) Molecular recognition<br>
3) QM/MM calculations<br>
4) QSAR<br>
5) ADMET<br>
<br>
Books published after 2000 would be great as it would cover the latest deve=
lopments.<br>
<br>
Thanks everyone for your time and valuable recommendations.<br>
<br>
Senthil Natesan,<br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-=
<br></div>=
; Conferences: <a href=3D"http://server.ccl.net/chemistry/announcements/con=
ferences/" target=3D"_blank">http://server.ccl.net/chemistry/announcements/=
conferences/</a>> <br>
</blockquote>
<br>
-------------------------------------------------<br>
Dr Florent Barbault<br>
Maitre de conferences / Assistant professor<br>
<br>
Universite Paris Diderot<br>
Laboratoire ITODYS<br>
15 rue Jean de Ba=C4=BCf, b=C4=81timent Lavoisier<br>
75013 Paris FRANCE<br>
<a href=3D"http://www.itodys.univ-paris7.fr/" target=3D"_blank">http://www.=
itodys.univ-paris7.fr/</a><br>
tel =C2=A0: (33) 01-57-27-88-50<br>
e-mail : florent.barbault=3D<a href=3D"http://univ-paris-diderot.fr" target=
=3D"_blank">univ-paris-diderot.fr</a><br>
-------------------------------------------------<div><div></div><div class=
=3D"h5"><br>
<br>
<br>
<br>
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</div></div></blockquote></div><div style=3D"margin: 0pt;" name=3D"sig_0f04=
1ac4c4"></div><br>
--001485f7cbee2a3d190481df3fd1--
From owner-chemistry@ccl.net Mon Mar 15 22:53:01 2010
From: "Yvonne Martin yvonnecmartin_+_gmail.com" <owner-chemistry%x%server.ccl.net>
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 <yvonnecmartin : gmail.com>
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
<owner-chemistry===ccl.net> 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
> <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 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" <owner-chemistry=3Dccl.n=
et>
>> 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" <owner-chemistry!=!server.ccl.net>
To: CCL
Subject: CCL: problem on g09
Message-Id: <-41443-100315211751-23398-/7FbA/XPK+YXQN80/Q18LA!=!server.ccl.net>
X-Original-From: "Xiaohui Kang" <huixiaokang328%163.com>
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