From owner-chemistry@ccl.net Mon May 16 01:03:00 2011 From: "ABHISHEK SHAHI shahi.abhishek1984 a gmail.com" To: CCL Subject: CCL: energy decomposition Message-Id: <-44639-110516005523-13954-z0CO5NnXUexk7qNFbnJZAg[a]server.ccl.net> X-Original-From: ABHISHEK SHAHI Content-Type: multipart/alternative; boundary=0016e6de1542d915b704a35d75f2 Date: Mon, 16 May 2011 10:25:11 +0530 MIME-Version: 1.0 Sent to CCL by: ABHISHEK SHAHI [shahi.abhishek1984 _ gmail.com] --0016e6de1542d915b704a35d75f2 Content-Type: text/plain; charset=ISO-8859-1 Dear All, I am looking for a free program for energy decomposition analysis of weakly interacted complexes (Like Molpro but its not free). Please suggest the same. Thanks in advance. ######################################################## *Using Gmail? Please read this important notice: http://www.fsf.org/campaigns/jstrap/gmail?28230.* ######################################################## With regards; *ABHISHEK SHAHI* *Research Scholar Inorganic and Physical Chemistry Indian Institute Of Science Bangalore-12* E-mail: shahi-x-ipc.iisc.ernet.in shahi.abhishek1984-x-gmail.com * * --0016e6de1542d915b704a35d75f2 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear All,

=A0=A0=A0 I am looking for a free program for energy deco= mposition analysis of weakly interacted complexes (Like Molpro but its not = free). Please suggest the same.

Thanks in advance.



=
#########################= ###############################
= Using Gmail? Please read this important notice: http://www.fsf.org/campaigns/j= strap/gmail?28230.
########################################################

With regards;<= br>=A0ABHISHEK SHAHI

Research ScholarInorganic= and Physical Chemistry
In= dian Institute Of Science
Bangalore-12
E-mail: =A0=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 shahi-x-ipc.iisc.ernet.in
=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 shahi.abhishek1984-x-gmail.com



--0016e6de1542d915b704a35d75f2-- From owner-chemistry@ccl.net Mon May 16 01:38:01 2011 From: "kimshu kanmo kimshukanmo[#]gmail.com" To: CCL Subject: CCL: name of journals Message-Id: <-44640-110515231624-27170-hH5AkmdZw1b344wN/CpgZQ-x-server.ccl.net> X-Original-From: "kimshu kanmo" Date: Sun, 15 May 2011 23:16:21 -0400 Sent to CCL by: "kimshu kanmo" [kimshukanmo^gmail.com] Hi Group, please help me in knowing the names of journals (besides established journals such as JPCA,JCP,PCCP,angew chem, JACS, IJQC, Theom.Chem. Acc) in which computational work can be published. thanks. kimshu korea From owner-chemistry@ccl.net Mon May 16 02:13:01 2011 From: "jessica Medina ysiquita65!=!hotmail.com" To: CCL Subject: CCL:G: gaussian DAPI Message-Id: <-44641-110515172652-1114-OdixjIiI30XsIYGC4FyTvg===server.ccl.net> X-Original-From: "jessica Medina" Date: Sun, 15 May 2011 17:26:49 -0400 Sent to CCL by: "jessica Medina" [ysiquita65 . hotmail.com] Hi everyone !!! I have a question and is how can I calculate the fluorescense of a molecule as DAPI 4',6-diamidino-2-phenylindole , using Gaussian? Wich is the better method to do that? and why? thanks !! From owner-chemistry@ccl.net Mon May 16 02:48:00 2011 From: "Min-Cheol Kim mckim.sinfire#,#gmail.com" To: CCL Subject: CCL:G: G03 MO printing format Message-Id: <-44642-110515225746-13056-STdvdGzwO2XglisF9/FbVA=-=server.ccl.net> X-Original-From: "Min-Cheol Kim" Date: Sun, 15 May 2011 22:57:43 -0400 Sent to CCL by: "Min-Cheol Kim" [mckim.sinfire(~)gmail.com] Hi, CCL subscribers. I'm trying to use the guess MO generated by Gaussian03 in other programs as the initial guess. Unfortunately, G03 prints the resulting MOs in normal format rather than exponential format: .. -------------------------------------------------------------- #p guess=(only, harris) nosymm geom=connectivity aug-cc-pvdz -------------------------------------------------------------- .. Alpha Molecular Orbital Coefficients 1 2 3 4 5 O O O O O EIGENVALUES -- -100.35508 -18.76328 -9.20459 -7.05543 -7.05531 1 1 Cl 1S 1.00099 -0.00005 -0.28256 0.00010 0.00000 2 2S -0.00384 -0.00049 1.04204 0.00034 0.00000 3 3S -0.00073 -0.00123 0.06846 0.00143 0.00000 4 4S 0.00080 0.00408 -0.04623 -0.00298 0.00000 5 5PX 0.00000 0.00000 0.00000 0.00000 0.47113 6 5PY 0.00000 0.00000 0.00000 0.00000 0.87696 7 5PZ 0.00001 0.00003 -0.00016 0.99535 0.00000 8 6PX 0.00000 0.00000 0.00000 0.00000 0.00672 9 6PY 0.00000 0.00000 0.00000 0.00000 0.01250 10 6PZ -0.00004 -0.00027 0.00208 0.01519 0.00000 .. but what I want is something like: .. 1: orbital energy = -.20251577D+02 .99421641D+00 .25847131D-01 .31906711D-02 .88241647D-15 .26760209D-02 -.55838749D-02 -.55838749D-02 .. The thing is if I'm uncomfortable converting the '0.00000' G03 numbers to '0.00000000D+00' numbers. Is there a way to print the G03 MO in the latter format? (I looked up the IOP options but nothing seemed relevant) Thank you in advance. From owner-chemistry@ccl.net Mon May 16 03:22:01 2011 From: "Chenghua Zhang zchua126.com[-]126.com" To: CCL Subject: CCL: name of journals Message-Id: <-44643-110516023543-27593-IT5yU+aQlyxYptlx98PlNA%a%server.ccl.net> X-Original-From: "Chenghua Zhang" Content-Type: multipart/alternative; boundary="----=_Part_164754_270848128.1305527728475" Date: Mon, 16 May 2011 14:35:28 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: "Chenghua Zhang" [zchua126.com-$-126.com] ------=_Part_164754_270848128.1305527728475 Content-Type: text/plain; charset=GBK Content-Transfer-Encoding: 7bit JMB,JBC,biochemistry,JPCB,Journal of Molecular Graphics and Modelling,... -- Sincerely Chenghua Zhang College of Chemistry Sichuan University, China. ------=_Part_164754_270848128.1305527728475 Content-Type: text/html; charset=GBK Content-Transfer-Encoding: 7bit
JMB,JBC,biochemistry,JPCB,Journal of Molecular Graphics and Modelling,...
--
Sincerely
Chenghua Zhang
College of Chemistry
Sichuan University, China.




------=_Part_164754_270848128.1305527728475-- From owner-chemistry@ccl.net Mon May 16 03:57:00 2011 From: "bonoit dahmani bonoit_10],[yahoo.fr" To: CCL Subject: CCL: Re : CCL: name of journals Message-Id: <-44644-110516025634-30847-imk67EHn3mQHKkjb7AhJWA a server.ccl.net> X-Original-From: bonoit dahmani Content-Type: multipart/alternative; boundary="0-475905011-1305528982=:45712" Date: Mon, 16 May 2011 07:56:22 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: bonoit dahmani [bonoit_10{=}yahoo.fr] --0-475905011-1305528982=:45712 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Kimshu, =A0 There are other journals for computational papers: JTCC ( Journal of theoretical and computational chemistry) TheoChem ( Journal iof theoretical chemistry) =A0 I wish that can help you Sincerely, Bonoit --- En date de=A0: Lun 16.5.11, kimshu kanmo kimshukanmo[#]gmail.com a =E9crit=A0: De: kimshu kanmo kimshukanmo[#]gmail.com Objet: CCL: name of journals =C0: "Bonoir, Bonoir " Date: Lundi 16 mai 2011, 5h16 Sent to CCL by: "kimshu=A0 kanmo" [kimshukanmo^gmail.com] Hi Group, please help me in knowing the names of journals (besides established journa= ls=20 such as JPCA,JCP,PCCP,angew chem, JACS, IJQC, Theom.Chem. Acc) in which=20 computational work can be published. thanks. kimshu korea -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0--0-475905011-1305528982=:45712 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable --0-475905011-1305528982=:45712-- From owner-chemistry@ccl.net Mon May 16 04:33:01 2011 From: "bonoit dahmani bonoit_10^_^yahoo.fr" To: CCL Subject: CCL: Re : CCL: energy decomposition Message-Id: <-44645-110516030141-11979-XbEXuf2NGvi7vzDi93syjg%%server.ccl.net> X-Original-From: bonoit dahmani Content-Type: multipart/alternative; boundary="0-1518184603-1305529291=:57267" Date: Mon, 16 May 2011 08:01:31 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: bonoit dahmani [bonoit_10_-_yahoo.fr] --0-1518184603-1305529291=:57267 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear ABHISHEK SHAHI , Try to use ORCA program, it's a free software. Sincerely, Bonoit --- En date de=A0: Lun 16.5.11, ABHISHEK SHAHI shahi.abhishek1984 a gmail.c= om a =E9crit=A0: De: ABHISHEK SHAHI shahi.abhishek1984 a gmail.com Objet: CCL: energy decomposition =C0: "Bonoir, Bonoir " Date: Lundi 16 mai 2011, 6h55 Dear All,=20 =A0=A0=A0 I am looking for a free program for energy decomposition analysis= of weakly interacted complexes (Like Molpro but its not free). Please sugg= est the same.=20 Thanks in advance.=20 ######################################################## Using Gmail? Please read this important notice: http://www.fsf.org/campaign= s/jstrap/gmail?28230. ######################################################## With regards; =A0ABHISHEK SHAHI Research Scholar Inorganic and Physical Chemistry Indian Institute Of Science Bangalore-12=20 E-mail: =A0=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 shahi[#]ipc.iisc.ernet.in =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0 shahi.abhishek1984[#]gmail.com --0-1518184603-1305529291=:57267 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Kimshu,
 
There are other journals for computational papers:
JTCC ( Journal of theoretical and computational chemistry)
TheoChem ( Journal iof theoretical chemistry)
 
I wish that can help you
Sincerely,
Bonoit

--- En date de : Lun 16.5.11, kimshu kanmo kimsh= ukanmo[#]gmail.com <owner-chemistry]=[ccl.net> a =E9crit&nbs= p;:

De: kimshu kanmo kimshukanmo[#]gmail.com <owne= r-chemistry]=[ccl.net>
Objet: CCL: name of journals
=C0: "Bonoir, Bo= noir " <bonoit_10]=[yahoo.fr>
Date: Lundi 16 mai 2011, 5h16

Sent to CCL by: "kimshu  kanmo" [kimshukanm= o^gmail.com]
Hi Group,
please help me in knowing the names of journal= s (besides established journals
such as JPCA,JCP,PCCP,angew chem, JACS,= IJQC, Theom.Chem. Acc) in which
computational work can be published.
thanks.
kimshu
korea



-=3D This is automatically = added to each message by the mailing script =3D-
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Dear ABHISHEK SHAHI ,
Try to use ORCA program, it's a free software.
Sincerely,
Bonoit

--- En date de : Lun 16.5.11, ABHISHEK SHAHI sha= hi.abhishek1984 a gmail.com <owner-chemistry(0)ccl.net> a = =E9crit :

De: ABHISHEK SHAHI shahi.abhishek1984 a gmail.com= <owner-chemistry(0)ccl.net>
Objet: CCL: energy decomposition
=C0= : "Bonoir, Bonoir " <bonoit_10(0)yahoo.fr>
Date: Lundi 16 mai= 2011, 6h55

Dear All,

    I am looking fo= r a free program for energy decomposition analysis of weakly interacted com= plexes (Like Molpro but its not free). Please suggest the same.

Tha= nks in advance.




##################################################= ######
Using Gmail? Please read this important notice: http:= //www.fsf.org/campaigns/jstrap/gmail?28230.
#######= #################################################

With regards;
 ABHISH= EK SHAHI

Research Scholar
Inorganic and Physical Chemistry
Indian Institute = Of Science
Bangalore-12
E-mail:  &nb= sp;               shahi[#]ipc.iisc.ernet.in
  &= nbsp;                &nbs= p;            shahi.= abhishek1984[#]gmail.com

To: CCL Subject: CCL: energy decomposition Message-Id: <-44646-110516035032-27017-m25xmzzjp/r3XxiLMoEmjg(!)server.ccl.net> X-Original-From: psavita:crlindia.com Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Date: Mon, 16 May 2011 13:25:50 +0530 MIME-Version: 1.0 MIME-Version: 1.0 Sent to CCL by: psavita..crlindia.com
Hello Abhishek,

The Morokuma analysis works well with co= mplexes of various kinds and is available with GAMESS U.S. that is freely d= ownloadable.

All the best,

Savita Pundlik
Computational Materi= als Applied Research Group
Computational Research Laboratories Ltd.,
Taco House, Damle Path, Off Law College Road=
Pune - 411004, India.



---= --owner-chemistry+psavita=3D=3Dcrlindia.com[#]ccl.net wrote: -----

To: "Pundlik, Sa= vita Sunil " <psavita[#]crlindia.com>
From: "ABHISHEK SHAHI= shahi.abhishek1984 a gmail.com" <owner-chemistry[#]ccl.net>
Sen= t by: owner-chemistry+psavita=3D=3Dcrlindia.co= m[#]ccl.net
Date: 05/16/2011 10:25AM
Subject: CCL: energy decomposi= tion

Dear All,

    I am looking for a free pr= ogram for energy decomposition analysis of weakly interacted complexes (Lik= e Molpro but its not free). Please suggest the same.

Thanks in adva= nce.




=0D########################################################=
=0DUsing Gmail? Please read this important notice: http://www.fsf.= org/campaigns/jstrap/gmail?28230.
=0D=0D####= ####################################################
=0D
With regards;
 ABHISHEK SHAHI

Researc= h Scholar
Inorganic and Physi= cal Chemistry
=0DIndian Insti= tute Of Science
Bangalore-12<= /font>
=0DE-mail:         =         sh= ahi[#]ipc.iisc.ernet.in
=0D    &n= bsp;                =            shahi.abhishek1984[#]gmail.com
= =0D


=0D=0D

= From owner-chemistry@ccl.net Mon May 16 05:44:00 2011 From: "psavita++crlindia.com" To: CCL Subject: CCL: name of journals Message-Id: <-44647-110516035835-6463-WzPAl+q2ObipMAJqZsUfWA()server.ccl.net> X-Original-From: psavita*crlindia.com Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Date: Mon, 16 May 2011 13:33:56 +0530 MIME-Version: 1.0 MIME-Version: 1.0 Sent to CCL by: psavita::crlindia.com
Hi,

A few names that come to me include CPL, Nano Letter= s, JOMC, JAP, J. of Comp.Chemistry (Physics, Biology, Materials),
J. of = Theoret. Physics, J. of Nanoscience (Nanosci. and Techn., Nanomaterials) et= c.

Have a good luck,

Savita Pundlik
Computational Materials Applied Research Group
Computational Research Laboratories Ltd.,
Taco House, Damle Path, Off Law College Road<= br style=3D"font-style: italic; font-family: Georgia,Default Serif,serif;">= Pune - 411004, India.=



-----owner-= chemistry+psavita=3D=3Dcrlindia.com!=!ccl.net wrote: -----

To: "Pundlik, Savita Sun= il " <psavita!=!crlindia.com>
From: "kimshu kanmo kimshukan= mo[#]gmail.com" <owner-chemistry!=!ccl.net>
Sent by: owner-chemistry+psavita=3D=3Dcrlindia.com!=!ccl.net
= Date: 05/16/2011 08:46AM
Subject: CCL: name of journals


Sent to CCL by: "kimshu =  kanmo" [kimshukanmo^gmail.com]
Hi Group,
please help me in know= ing the names of journals (besides established journals
such as JPCA,JC= P,PCCP,angew chem, JACS, IJQC, Theom.Chem. Acc) in which
computational = work can be published.

thanks.
kimshu
korea



-= =3D This is automatically added to each message by the mailing script =3D-<= br= l= ook up the X-Original-From: line in the mail header.

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=0D

= From owner-chemistry@ccl.net Mon May 16 07:39:00 2011 From: "Vincent Leroux vincent.leroux()loria.fr" To: CCL Subject: CCL: Re : CCL: name of journals Message-Id: <-44648-110516071735-16992-IvAJbr+Q0jbpCp5LDjYSvA() server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 16 May 2011 13:05:48 +0200 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux_+_loria.fr] Hello, Other computational chemistry-oriented journals: - J Chem Inf Model - J Comput Chem - J Mol Graph Model - J Mol Mod - J Mol Struct (different from J Mol Struct-Theochem) - J Comput-Aided Drug Des (if your work relates to drug design) I can also suggest those, not exclusively dedicated to computational chemistry work, but quite friendly: - PLoS One (if your work is good!) - PLoS Comput Biol (good work + bioinformatics-related) - Chem Biol Drug Des - Adv Appl Bioinf Chem (new open-access journal: http://www.dovepress.com/advances-and-applications-in-bioinformatics-and-chemistry-journal) Regards VL Le 16/05/11 08:56, bonoit dahmani bonoit_10],[yahoo.fr a écrit : > Dear Kimshu, > > There are other journals for computational papers: > JTCC ( Journal of theoretical and computational chemistry) > TheoChem ( Journal iof theoretical chemistry) > > I wish that can help you > Sincerely, > Bonoit > > --- En date de : Lun 16.5.11, kimshu kanmo kimshukanmo[#]gmail.com a écrit : > > > De: kimshu kanmo kimshukanmo[#]gmail.com > Objet: CCL: name of journals > À: "Bonoir, Bonoir " > Date: Lundi 16 mai 2011, 5h16 > > > > Sent to CCL by: "kimshu kanmo" [kimshukanmo^gmail.com] > Hi Group, > please help me in knowing the names of journals (besides established journals > such as JPCA,JCP,PCCP,angew chem, JACS, IJQC, Theom.Chem. Acc) in which > computational work can be published. > > thanks. > kimshu > korea--0-475905011-1305528982=:45712 > Content-Type: text/html; charset=iso-8859-1 > Content-Transfer-Encoding: quoted-printable > >
Dear Kimshu,
>
 
>
There are other journals for computational papers:
>
JTCC ( Journal of theoretical and computational chemistry)
>
TheoChem ( Journal iof theoretical chemistry)
>
 
>
I wish that can help you
>
Sincerely,
>
Bonoit

--- En date de :Lun 16.5.11, kimshu kanmo kimshukanmo[#]gmail.com<owner-chemistry::ccl.net> a écrit :
>

De: kimshu kanmo kimshukanmo[#]gmail.com<owner-chemistry::ccl.net>
Objet: CCL: name of journals
À: "Bonoir, Bonoir "<bonoit_10::yahoo.fr>
Date: Lundi 16 mai 2011, 5h16

>

Sent to CCL by: "kimshu  kanmo" [kimshukanmo^gmail.com]
Hi Group,
please help me in knowing the names of journals (besides established journals
such as JPCA,JCP,PCCP,angew chem, JACS, IJQC, Theom.Chem. Acc) in which
computational work can be published.

thanks.
kimshu
korea


the strange characters on the top line to the :: sign. You can also
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From owner-chemistry@ccl.net Mon May 16 08:16:00 2011 From: "Ulrike Salzner salzner()fen.bilkent.edu.tr" To: CCL Subject: CCL:G: Chemissian Message-Id: <-44649-110516023949-6093-2wRwpJ7st8wW+FLlbl6Vtg+/-server.ccl.net> X-Original-From: Ulrike Salzner Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 16 May 2011 09:39:42 +0300 MIME-Version: 1.0 Sent to CCL by: Ulrike Salzner [salzner[*]fen.bilkent.edu.tr] Hello, I have downloaded the trial version of "Chemissian" to plot electron density differences between anions and neutral species from G09 calculations. I am using the gfinput, p and pop=full keywords. Upon opening the files I get a window saying "error reading basis set". I tried also G03 to see whether there is a version problem. Did not work either. Does anyone know how to get around this or is there any other program for Windows or LINUX that can do such plots? Thank in advance, Ulrike -- Assoc. Prof. Ulrike Salzner Department of Chemistry Bilkent University 06800 Bilkent, Ankara From owner-chemistry@ccl.net Mon May 16 08:51:00 2011 From: "Andreas Uhe andreas.uhe{}rwth-aachen.de" To: CCL Subject: CCL: name of journals Message-Id: <-44650-110516024442-11192-rJ6uWjhxiWd+5G17dcRIog]~[server.ccl.net> X-Original-From: Andreas Uhe Content-transfer-encoding: 7BIT Content-type: text/plain; charset=ISO-8859-15; format=flowed Date: Mon, 16 May 2011 08:44:16 +0200 MIME-version: 1.0 Sent to CCL by: Andreas Uhe [andreas.uhe|*|rwth-aachen.de] Dear Kimshu, the Journal of Computational Chemistry (JCC) and the Journal of Chemical Theory and Computation (JCTC) are further options. Computational works are also accepted for publication in Chemistry - A European Journal. Kind regards, Andi Am 16.05.2011 05:16, schrieb kimshu kanmo kimshukanmo[#]gmail.com: > Sent to CCL by: "kimshu kanmo" [kimshukanmo^gmail.com] > Hi Group, > please help me in knowing the names of journals (besides established journals > such as JPCA,JCP,PCCP,angew chem, JACS, IJQC, Theom.Chem. Acc) in which > computational work can be published. > > thanks. > kimshu > korea> > > From owner-chemistry@ccl.net Mon May 16 09:26:00 2011 From: "David A Mannock dmannock]=[ualberta.ca" To: CCL Subject: CCL: To begin with computational chemistry Message-Id: <-44651-110515172806-7224-+B9LyJaL94XpOt5f2i/kcQ : server.ccl.net> X-Original-From: David A Mannock Content-Type: multipart/alternative; boundary=20cf307f37c8513cce04a35736a2 Date: Sun, 15 May 2011 15:27:55 -0600 MIME-Version: 1.0 Sent to CCL by: David A Mannock [dmannock a ualberta.ca] --20cf307f37c8513cce04a35736a2 Content-Type: text/plain; charset=ISO-8859-1 Oops! Thanks for that correction. I had deleted the message containing the link. Dave On Sun, May 15, 2011 at 1:26 AM, Dr. Bhargav Trivedi bhargavatrivedi* gmail.com wrote: > For your kind attention, the site was Indonesian and not Indian. > > On Sat, May 7, 2011 at 2:42 AM, David A Mannock dmannock]*[ualberta.ca < > owner-chemistry^-^ccl.net> wrote: > >> Anurikta, Put your moral indignation aside for the moment. Yes, piracy >> happens everywhere, but we are not talking about soccer games here, but text >> books and software. Many of the major computer chemistry software programs >> come from Western companies and texts relevant to that software generally >> cost more money than is available to a student in a third world country. If >> I borrow something > from the internet as a trial or an illegal copy, I try >> out the software or book and if it is useful, I go ahead with a personal >> purchase (Yes, out of my own pocket!!) or get something through my >> institution. Incidentally, I have purchased lower priced texts of interest >> to me from publishers in India and they are similar in price to the Dover >> classics available on Amazon. The difference in price is an order of >> magnitude. My focus on China and India is simply that there have been many >> news items here over the past 10 years about exactly this type of piracy and >> the reluctance of the respective institutions and governments to take >> positive steps to eliminate it. What I am saying is that I understand the >> need for students in non-western countries to get what they need to have an >> education. Research and higher education is expensive and even in countries >> like Canada, money for such things is very tight. >> >> Part of the piracy problem is that some publishing houses are trying to >> cut costs by outsourcing the printing of the books, presumably through the >> transfer of electronic media to those countries. One of the arguments that I >> have made here is for proper assertion of the rights of authorship through >> the universities commercial offices and publishing houses to stamp out >> institutional piracy. It was pointed out on this forum that the web site on >> which Prof Cramer's book was stored was at an Indian institution. I suspect >> that a blind eye is turned to such practices by both the institution and the >> local government. Here it is feasible for the publishing or software company >> or the author to make the accusation of plagiarism or piracy in the civil >> court and sue. This is not easily done in other countries and the amount of >> any settlement may itself be dictated by the local market rather than the >> market where the product was developed. If you feel strongly that this >> practice should be stamped out in your own institution, try approaching your >> VP research and see if you can accomplish this. My guess is that you will >> receive nothing more than lip-service from the senior administration and >> that no one will want to touch this issue with a barge pole. >> >> Here on my lab computers, I am not permitted to install illegal copies of >> software and as a general rule, I do not download textbooks that I do not >> consider for purchase. When my responsibilities for writing up manuscripts >> ends here and I have to find a job elsewhere, all university licensed >> software will need to be uninstalled from my lab and home computers. In >> fact, I was reminded of this by our IT support person this week. Today, >> everyone wants their buck. There is no escaping this. Dave >> >> >> > > > -- > Dr. Bhargav Trivedi, > Associate Professor Of Chemistry, > J & J College Of Science, > Nadiad, Gujarat. > India. > Phone: +919825654872 > > --20cf307f37c8513cce04a35736a2 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Oops! Thanks for that correction. I had deleted the message containing the = link. Dave

On Sun, May 15, 2011 at 1:26 A= M, Dr. Bhargav Trivedi bhargavatrivedi*gmail.c= om <own= er-chemistry(a)ccl.net> wrote:
For your kind attention, the site was Indon= esian and not Indian.

On Sat, May 7, 201= 1 at 2:42 AM, David A Mannock dmannock]*[ualberta.ca <owner-chemistry^-^ccl.net&= gt; wrote:
Anurikta, Put your mora= l indignation aside for the moment. Yes, piracy happens everywhere, but we = are not talking about soccer games here, but text books and software. Many = of the major computer chemistry software programs come from Western compani= es and texts relevant to that software generally cost more money than is av= ailable to a student in a third world country. If I borrow something > f= rom the internet as a trial or an illegal copy, I try out the software or b= ook and if it is useful, I go ahead with a personal purchase (Yes, out of m= y own pocket!!) or get something through my institution. Incidentally, I ha= ve purchased lower priced texts of interest to me from publishers in India = and they are similar in price to the Dover classics available on Amazon. Th= e difference in price is an order of magnitude. My focus on China and India= is simply that there have been many news items here over the past 10 years= about exactly this type of piracy and the reluctance of the respective ins= titutions and governments to take positive steps to eliminate it. What I am= saying is that I understand the need for students in non-western countries= to get what they need to have an education. Research and higher education = is expensive and even in countries like Canada, money for such things is ve= ry tight.

Part of the piracy problem is that some publishing houses are trying to= cut costs by outsourcing the printing of the books, presumably through the= transfer of electronic media to those countries. One of the arguments that= I have made here is for proper assertion of the rights of authorship throu= gh the universities commercial offices and publishing houses to stamp out i= nstitutional piracy. It was pointed out on this forum that the web site on = which Prof Cramer's book was stored was at an Indian institution. I sus= pect that a blind eye is turned to such practices by both the institution a= nd the local government. Here it is feasible for the publishing or software= company or the author to make the accusation of plagiarism or piracy in th= e civil court and sue. This is not easily done in other countries and the a= mount of any settlement may itself be dictated by the local market rather t= han the market where the product was developed. If you feel strongly that t= his practice should be stamped out in your own institution, try approaching= your VP research and see if you can accomplish this. My guess is that you = will receive nothing more than lip-service from the senior administration a= nd that no one will want to touch this issue with a barge pole.

Here on my lab computers, I am not permitted to install illegal copies = of software and as a general rule, I do not download textbooks that I do no= t consider for purchase. When my responsibilities for writing up manuscript= s ends here and I have to find a job elsewhere, all university licensed sof= tware will need to be uninstalled from my lab and home computers. In fact, = I was reminded of this by our IT support person this week. Today, everyone = wants their buck. There is no escaping this. Dave





--
Dr. Bhargav Trivedi,Associate Professor Of Chemistry,
J & J College Of Science,
Nadi= ad, Gujarat.
India.
Phone: +919825654872


--20cf307f37c8513cce04a35736a2-- From owner-chemistry@ccl.net Mon May 16 10:01:01 2011 From: "Praveen Kumar Shrivastava praveenshrivastav*gmail.com" To: CCL Subject: CCL: To begin with computational chemistry Message-Id: <-44652-110516043555-561-lr/tBxSHL0tZUUqLF7Jzfw*|*server.ccl.net> X-Original-From: Praveen Kumar Shrivastava Content-Type: multipart/alternative; boundary=90e6ba6137c28d574b04a3608a21 Date: Mon, 16 May 2011 14:05:43 +0530 MIME-Version: 1.0 Sent to CCL by: Praveen Kumar Shrivastava [praveenshrivastav-#-gmail.com] --90e6ba6137c28d574b04a3608a21 Content-Type: text/plain; charset=ISO-8859-1 Dear Dr Trivedi I agree with your view. For this we have produce good software as well as write god textbook. Then only this type incident will never happens. Blaming other will not do. We have to come do it or developing software. With my best wishes Praveen On Sun, May 15, 2011 at 12:56 PM, Dr. Bhargav Trivedi bhargavatrivedi* gmail.com wrote: > For your kind attention, the site was Indonesian and not Indian. > > On Sat, May 7, 2011 at 2:42 AM, David A Mannock dmannock]*[ualberta.ca < > owner-chemistry^-^ccl.net> wrote: > >> Anurikta, Put your moral indignation aside for the moment. Yes, piracy >> happens everywhere, but we are not talking about soccer games here, but text >> books and software. Many of the major computer chemistry software programs >> come from Western companies and texts relevant to that software generally >> cost more money than is available to a student in a third world country. If >> I borrow something > from the internet as a trial or an illegal copy, I try >> out the software or book and if it is useful, I go ahead with a personal >> purchase (Yes, out of my own pocket!!) or get something through my >> institution. Incidentally, I have purchased lower priced texts of interest >> to me from publishers in India and they are similar in price to the Dover >> classics available on Amazon. The difference in price is an order of >> magnitude. My focus on China and India is simply that there have been many >> news items here over the past 10 years about exactly this type of piracy and >> the reluctance of the respective institutions and governments to take >> positive steps to eliminate it. What I am saying is that I understand the >> need for students in non-western countries to get what they need to have an >> education. Research and higher education is expensive and even in countries >> like Canada, money for such things is very tight. >> >> Part of the piracy problem is that some publishing houses are trying to >> cut costs by outsourcing the printing of the books, presumably through the >> transfer of electronic media to those countries. One of the arguments that I >> have made here is for proper assertion of the rights of authorship through >> the universities commercial offices and publishing houses to stamp out >> institutional piracy. It was pointed out on this forum that the web site on >> which Prof Cramer's book was stored was at an Indian institution. I suspect >> that a blind eye is turned to such practices by both the institution and the >> local government. Here it is feasible for the publishing or software company >> or the author to make the accusation of plagiarism or piracy in the civil >> court and sue. This is not easily done in other countries and the amount of >> any settlement may itself be dictated by the local market rather than the >> market where the product was developed. If you feel strongly that this >> practice should be stamped out in your own institution, try approaching your >> VP research and see if you can accomplish this. My guess is that you will >> receive nothing more than lip-service from the senior administration and >> that no one will want to touch this issue with a barge pole. >> >> Here on my lab computers, I am not permitted to install illegal copies of >> software and as a general rule, I do not download textbooks that I do not >> consider for purchase. When my responsibilities for writing up manuscripts >> ends here and I have to find a job elsewhere, all university licensed >> software will need to be uninstalled from my lab and home computers. In >> fact, I was reminded of this by our IT support person this week. Today, >> everyone wants their buck. There is no escaping this. Dave >> >> >> > > > -- > Dr. Bhargav Trivedi, > Associate Professor Of Chemistry, > J & J College Of Science, > Nadiad, Gujarat. > India. > Phone: +919825654872 > > --90e6ba6137c28d574b04a3608a21 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Dr Trivedi

I agree with your view. F= or this we have produce good software as well as write god textbook. Then o= nly this type incident will never happens.
Blaming other will not= do. We have to come do it =A0or developing software.=A0
With my best wishes
Praveen

On Sun, May 15, 2011 at 12:56 PM, Dr. Bhargav Trivedi bhargavatrivedi*<= a href=3D"http://gmail.com">gmail.com <owner-chemistry^ccl.net> wrot= e:
For your kind attention, the site was Indon= esian and not Indian.

On Sat, May 7, 201= 1 at 2:42 AM, David A Mannock dmannock]*[ualberta.ca <owner-chemistry^-^ccl.net&= gt; wrote:
Anurikta, Put your mora= l indignation aside for the moment. Yes, piracy happens everywhere, but we = are not talking about soccer games here, but text books and software. Many = of the major computer chemistry software programs come from Western compani= es and texts relevant to that software generally cost more money than is av= ailable to a student in a third world country. If I borrow something > f= rom the internet as a trial or an illegal copy, I try out the software or b= ook and if it is useful, I go ahead with a personal purchase (Yes, out of m= y own pocket!!) or get something through my institution. Incidentally, I ha= ve purchased lower priced texts of interest to me from publishers in India = and they are similar in price to the Dover classics available on Amazon. Th= e difference in price is an order of magnitude. My focus on China and India= is simply that there have been many news items here over the past 10 years= about exactly this type of piracy and the reluctance of the respective ins= titutions and governments to take positive steps to eliminate it. What I am= saying is that I understand the need for students in non-western countries= to get what they need to have an education. Research and higher education = is expensive and even in countries like Canada, money for such things is ve= ry tight.

Part of the piracy problem is that some publishing houses are trying to= cut costs by outsourcing the printing of the books, presumably through the= transfer of electronic media to those countries. One of the arguments that= I have made here is for proper assertion of the rights of authorship throu= gh the universities commercial offices and publishing houses to stamp out i= nstitutional piracy. It was pointed out on this forum that the web site on = which Prof Cramer's book was stored was at an Indian institution. I sus= pect that a blind eye is turned to such practices by both the institution a= nd the local government. Here it is feasible for the publishing or software= company or the author to make the accusation of plagiarism or piracy in th= e civil court and sue. This is not easily done in other countries and the a= mount of any settlement may itself be dictated by the local market rather t= han the market where the product was developed. If you feel strongly that t= his practice should be stamped out in your own institution, try approaching= your VP research and see if you can accomplish this. My guess is that you = will receive nothing more than lip-service from the senior administration a= nd that no one will want to touch this issue with a barge pole.

Here on my lab computers, I am not permitted to install illegal copies = of software and as a general rule, I do not download textbooks that I do no= t consider for purchase. When my responsibilities for writing up manuscript= s ends here and I have to find a job elsewhere, all university licensed sof= tware will need to be uninstalled from my lab and home computers. In fact, = I was reminded of this by our IT support person this week. Today, everyone = wants their buck. There is no escaping this. Dave





--
Dr. Bhargav Trivedi,Associate Professor Of Chemistry,
J & J College Of Science,
Nadi= ad, Gujarat.
India.
Phone: +919825654872


--90e6ba6137c28d574b04a3608a21-- From owner-chemistry@ccl.net Mon May 16 10:35:01 2011 From: "=?iso-8859-1?Q?Jordi_Vill=E0_i_Freixa?= jordi.villafreixa ~ gmail.com" To: CCL Subject: CCL: Re : CCL: name of journals Message-Id: <-44653-110516090801-16559-VhHFY1DZjbVXN/y0zzwM2A _ server.ccl.net> X-Original-From: =?iso-8859-1?Q?Jordi_Vill=E0_i_Freixa?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Mon, 16 May 2011 15:07:33 +0200 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: =?iso-8859-1?Q?Jordi_Vill=E0_i_Freixa?= [jordi.villafreixa---gmail.com] check also the new Molecular Informatics journal http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1868-1751 On May 16, 2011, at 1:05 PM, Vincent Leroux vincent.leroux()loria.fr wrote: > > Sent to CCL by: Vincent Leroux [vincent.leroux_+_loria.fr] > Hello, > > Other computational chemistry-oriented journals: > - J Chem Inf Model > - J Comput Chem > - J Mol Graph Model > - J Mol Mod > - J Mol Struct (different from J Mol Struct-Theochem) > - J Comput-Aided Drug Des (if your work relates to drug design) > > I can also suggest those, not exclusively dedicated to computational > chemistry work, but quite friendly: > > - PLoS One (if your work is good!) > - PLoS Comput Biol (good work + bioinformatics-related) > - Chem Biol Drug Des > - Adv Appl Bioinf Chem (new open-access journal: > http://www.dovepress.com/advances-and-applications-in-bioinformatics-and-chemistry-journal) > > Regards > VL > > > Le 16/05/11 08:56, bonoit dahmani bonoit_10],[yahoo.fr a écrit : >> Dear Kimshu, >> >> There are other journals for computational papers: >> JTCC ( Journal of theoretical and computational chemistry) >> TheoChem ( Journal iof theoretical chemistry) >> >> I wish that can help you >> Sincerely, >> Bonoit >> >> --- En date de : Lun 16.5.11, kimshu kanmo kimshukanmo[#]gmail.com a écrit : >> >> >> De: kimshu kanmo kimshukanmo[#]gmail.com >> Objet: CCL: name of journals >> À: "Bonoir, Bonoir " >> Date: Lundi 16 mai 2011, 5h16 >> >> >> >> Sent to CCL by: "kimshu kanmo" [kimshukanmo^gmail.com] >> Hi Group, >> please help me in knowing the names of journals (besides established journals >> such as JPCA,JCP,PCCP,angew chem, JACS, IJQC, Theom.Chem. Acc) in which >> computational work can be published. >> >> thanks. >> kimshu >> korea--0-475905011-1305528982=:45712 >> Content-Type: text/html; charset=iso-8859-1 >> Content-Transfer-Encoding: quoted-printable >> >>
Dear Kimshu,
>>
 
>>
There are other journals for computational papers:
>>
JTCC ( Journal of theoretical and computational chemistry)
>>
TheoChem ( Journal iof theoretical chemistry)
>>
 
>>
I wish that can help you
>>
Sincerely,
>>
Bonoit

--- En date de :Lun 16.5.11, kimshu kanmo kimshukanmo[#]gmail.com<owner-chemistry::ccl.net> a écrit :
>>

De: kimshu kanmo kimshukanmo[#]gmail.com<owner-chemistry::ccl.net>
Objet: CCL: name of journals
À: "Bonoir, Bonoir "<bonoit_10::yahoo.fr>
Date: Lundi 16 mai 2011, 5h16

>>

Sent to CCL by: "kimshu  kanmo" [kimshukanmo^gmail.com]
Hi Group,
please help me in knowing the names of journals (besides established journals
such as JPCA,JCP,PCCP,angew chem, JACS, IJQC, Theom.Chem. Acc) in which
computational work can be published.

thanks.
kimshu
korea


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> -- Jordi Villà i Freixa Computational Biochemistry and Biophysics lab Research Group on Biomedical Informatics (GRIB) - IMIM/UPF Parc de Recerca Biomèdica de Barcelona C/ Doctor Aiguader, 88; 08003 Barcelona (Spain) Tel: +34 93 316 0504 // Fax: +34 93 316 0550 e-mail: jvilla||imim.es http://cbbl.imim.es From owner-chemistry@ccl.net Mon May 16 11:10:00 2011 From: "Jason Rigby Jason.Rigby-x-monash.edu" To: CCL Subject: CCL: energy decomposition Message-Id: <-44654-110516015151-26875-ABM7AaeGMA8f1nr7GIp0QQ%%server.ccl.net> X-Original-From: Jason Rigby Content-Type: multipart/alternative; boundary=0023545bd690d7796104a35e3fcf Date: Mon, 16 May 2011 00:51:20 -0500 MIME-Version: 1.0 Sent to CCL by: Jason Rigby [Jason.Rigby]=[monash.edu] --0023545bd690d7796104a35e3fcf Content-Type: text/plain; charset=ISO-8859-1 You could try the Morokuma-Kitaura analysis, LMOEDA method or EFP method as implemented in GAMESS. Or depending on how large your system is, you could also give SAPT a go... But to my knowledge it doesn't run in parallel very well (if at all) so only small systems are feasible. Best of luck Jason On Sun, May 15, 2011 at 11:55 PM, ABHISHEK SHAHI shahi.abhishek1984 a gmail.com wrote: > Dear All, > > I am looking for a free program for energy decomposition analysis of > weakly interacted complexes (Like Molpro but its not free). Please suggest > the same. > > Thanks in advance. > > > > > ######################################################## > *Using Gmail? Please read this important notice: > http://www.fsf.org/campaigns/jstrap/gmail?28230.* > ######################################################## > > With regards; > *ABHISHEK SHAHI* > > *Research Scholar > Inorganic and Physical Chemistry > Indian Institute Of Science > Bangalore-12* > E-mail: shahi[#]ipc.iisc.ernet.in > shahi.abhishek1984[#]gmail.com > * > * > > --0023545bd690d7796104a35e3fcf Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable You could try the Morokuma-Kitaura analysis, LMOEDA method or EFP method as= implemented in GAMESS. Or depending on how large your system is, you could= also give SAPT a go... =A0But to my knowledge it doesn't run in parall= el very well (if at all) so only small systems are=A0feasible.

Best of luck
Jason

On Sun, May 15, 2011 at 11:55 PM, ABHISHEK SHAHI shahi.abhishek1984 a <= a href=3D"http://gmail.com">gmail.com <owner-chemistry[A]ccl.net> wrot= e:
Dear All,

=A0=A0=A0 I am looking fo= r a free program for energy decomposition analysis of weakly interacted com= plexes (Like Molpro but its not free). Please suggest the same.

Thanks in advance.




#########################= ###############################
= Using Gmail? Please read this important notice: http://www.fsf.org/campaigns/j= strap/gmail?28230.
########################################################

With regards;<= br>=A0ABHISHEK SHAHI

Research ScholarInorganic= and Physical Chemistry
In= dian Institute Of Science
Bangalore-12
E-mail: =A0=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 shahi[#]ipc.iisc.ernet.in
=A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 shahi.abhishek1984[#]gmail.com




--0023545bd690d7796104a35e3fcf-- From owner-chemistry@ccl.net Mon May 16 11:45:00 2011 From: "Shirley Peng speng:chemcomp.com" To: CCL Subject: CCL: MOE workshops - Antibodies/MedChem/Kinases - San Diego Message-Id: <-44655-110516102526-743-oRkMn8b9blMgjp6ct8/IJQ||server.ccl.net> X-Original-From: "Shirley Peng" Date: Mon, 16 May 2011 10:25:23 -0400 Sent to CCL by: "Shirley Peng" [speng/./chemcomp.com] Reminder about the coming hands-on workshop sessions in San Diego June 2, 2011. The workshops are free but pre-registration is required. To register for any of the sessions, please go to http://www.chemcomp.com/workshops-sd2.htm. MOE WORKSHOPS > SAN DIEGO > June 2, 2011 ======================================================================== Session 1 MOE for Medicinal Chemists 9:00 am to 12:00 am Ligand optimization in pocket ------------------------------------------------------------------------ Session 2 Antibody Modeling 1:00 pm to 4:00 pm Template selection |Superpositions | CDR Analysis ------------------------------------------------------------------------ Session 3 Kinase Data Mining and Modeling 4:00 pm to 5:00 pm Structure database search | Template selection | Loop modeling ======================================================================== Where: UCSD Extension 6925 Lusk Blvd., San Diego, CA 92121 MAP ======================================================================== Feel free to forward this email to anyone interested in the subject. We look forward to meeting you during the workshop! Have a great day, Shirley Shirley Peng Marketing Assistant Chemical Computing Group 1010 Sherbrooke St. W, Suite 910 Montreal, Quebec, Canada H3A 2R7 Tel: 514-393-1055146 | Fax: 514-874-9538 speng()chemcomp.com | www.chemcomp.com * * * * * * * * * * * * * * * * * * * * * * * * * * * NORTH AMERICAN USER GROUP MEETING 2011 June 20-21 / Training & One-on-One Sessions June 22-23 / Scientific Presentations Montreal, Canada http://www.chemcomp.com/ugm-2011.htm * * * * * * * * * * * * * * * * * * * ** * * * * * * From owner-chemistry@ccl.net Mon May 16 12:21:01 2011 From: "David Livingstone davel a chemquestuk.com" To: CCL Subject: CCL: Chemoinformatics Message-Id: <-44656-110516085344-32342-f8yH8uBjqutyLPJAUkMwsA{}server.ccl.net> X-Original-From: "David Livingstone" Content-description: Mail message body Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=ISO-8859-1 Date: Mon, 16 May 2011 13:54:02 +0100 MIME-Version: 1.0 Sent to CCL by: "David Livingstone" [davel---chemquestuk.com] Dear All, > Dear CCLrs, >   > Recently my faculty is considering to offer an undergraduate course on > Chemoinformatics, for chemistry students. Though I´ve been working a bit > on computational chemistry, I do not feel I have the proper vision to > built up a syllabus proposal, or even for giving a reasonable criticism of > anyone else proposal.   I would really appreciate your opinion on > what should be included in a course of such a level? After the recent debate here on books and piracy which got quite heated at times I'm hesitant to suggest this! Following numerous requests from colleagues and students to recommend a book on statistics for quantitative drug design I wrote one myself in 1995. I revised and updated this to make it more generally applicable (and perhaps appeal to a wider audience?) and it was published by Wiley in 2009 (ISBN 978-0-470-85153-1). You can see the contents on my website at http://www.chemquestuk.com/page20a.html. It might be something that your students find useful and/or may be of some help in structuring your course. Regards, David L -- D.J. Livingstone ChemQuest Delamere House, 1 Royal Crescent, Sandown. Isle of Wight UK PO36 8LZ Phone: +44 (0)1983 406832 e-mail davel[A]chemquestuk.com www.chemquestuk.com ------------------------------------------------------------------ From owner-chemistry@ccl.net Mon May 16 12:56:00 2011 From: "Guntram Schmidt guntram.schmidt(-)chemie.uni-halle.de" To: CCL Subject: CCL:G: Tool to autocorrect hydrogen-positions from xray-structures? Message-Id: <-44657-110516104640-4401-MmonEiKqA90YuluI7WZEag _ server.ccl.net> X-Original-From: "Guntram Schmidt" Date: Mon, 16 May 2011 10:46:37 -0400 Sent to CCL by: "Guntram Schmidt" [guntram.schmidt+*+chemie.uni-halle.de] Dear subscribers, as it is well established, the bond length of light elements in crystal structures are shortened due to effects like libration. Is there any tool, to correct these bond length to "real" values, especially for hydrogen atoms? Doing a partial optimization with gaussian is no fun anymore with bigger structures and having to sort the atoms by hand to group all hydrogens. Thanks a lot for hints on this, Guntram From owner-chemistry@ccl.net Mon May 16 13:31:00 2011 From: "Goedele Roos groos(-)vub.ac.be" To: CCL Subject: CCL: hydrophobicity scale Message-Id: <-44658-110516130523-708-oqEwjiEV4zsx98DZWEnpBg*server.ccl.net> X-Original-From: Goedele Roos Date: Mon, 16 May 2011 19:05:07 +0200 Sent to CCL by: Goedele Roos [groos : vub.ac.be] Hi all, Does anyone know a good hydrophobicity scale for small molecules like CH4 and H2O? Thank you in advance, Goedele _____________________________ Goedele Roos, PhD Department of General Chemistry VIB Department of Molecular and Cellular Interactions | http://www.vib.be/ Structural Biology Brussels, Vrije Universiteit Brussel | http://www.structuralbiology.be/ Brussels Center for Redox Biology | http://redox.vub.ac.be/ Vrije Universiteit Brussel, Building G, room 10G714 Pleinlaan 2, 1050 Brussels,Belgium phone: +32 2 6293312 fax: +32 2 6293317 E-mail: groos]|[vub.ac.be From owner-chemistry@ccl.net Mon May 16 14:06:00 2011 From: "Eduard Matito ematito*gmail.com" To: CCL Subject: CCL:G: energy decomposition Message-Id: <-44659-110516055805-27985-qNX4UiZ3bU6KY/VwEzfYwA^server.ccl.net> X-Original-From: Eduard Matito Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Mon, 16 May 2011 11:57:50 +0200 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Eduard Matito [ematito:gmail.com] There was a similar discussion in CCL four months ago... I said: Istvan Mayer and Pedro Salvador have some programs to perform an energy decomposition analysis. They are free. Most of them use gaussian files (fchk or similar). http://occam.chemres.hu/programs/ Eduard On May 16, 2011, at 9:55 AM, psavita,,crlindia.com wrote: > Sent to CCL by: psavita..crlindia.com > Hello Abhishek, > > The Morokuma analysis works well with complexes of various kinds and > is available with GAMESS U.S. that is freely downloadable. > > All the best, > > Savita Pundlik > Computational Materials Applied Research Group > Computational Research Laboratories Ltd., > Taco House, Damle Path, Off Law College Road > Pune - 411004, India. > > > > -----owner-chemistry+psavita==crlindia.com^^^ccl.net wrote: ----- > > To: "Pundlik, Savita Sunil " > From: "ABHISHEK SHAHI shahi.abhishek1984 a gmail.com" chemistry^^^ccl.net> > Sent by: owner-chemistry+psavita==crlindia.com^^^ccl.net > Date: 05/16/2011 10:25AM > Subject: CCL: energy decomposition > > Dear All, > > I am looking for a free program for energy decomposition > analysis of weakly interacted complexes (Like Molpro but its not > free). Please suggest the same. > > Thanks in advance. > > > > > ######################################################## > Using Gmail? Please read this important notice: http://www.fsf.org/campaigns/jstrap/gmail?28230 > . > ######################################################## > > With regards; > ABHISHEK SHAHI > > Research Scholar > Inorganic and Physical Chemistry > Indian Institute Of Science > Bangalore-12 > E-mail: shahi[#]ipc.iisc.ernet.in > shahi.abhishek1984[#]gmail.com > > > > > - This is automatically added to each message by the mailing script > =- To recover the email address of the author of the message, please > change the strange characters on the top line to the .:. sign. You can > alsoE-mail to > subscribers: CHEMISTRY.:.ccl.net or use:http://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-- Eduard Matito Postdoctoral researcher Kimika Fakultatea Euskal Herriko Unibersitatea (University of the Basque Country) 20080 Donostia (Euskal Herria) Phone: +34943015341 http://ematito.webs.com From owner-chemistry@ccl.net Mon May 16 14:41:00 2011 From: "Mahmoud E. Soliman askambermail###gmail.com" To: CCL Subject: CCL: name of journals Message-Id: <-44660-110516104005-29909-GsyM0a05gkrt1AbOzjm9Zw{:}server.ccl.net> X-Original-From: "Mahmoud E. Soliman" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Mon, 16 May 2011 16:40:43 +0300 MIME-Version: 1.0 Sent to CCL by: "Mahmoud E. Soliman" [askambermail_-_gmail.com] I would also suggest: OBC ; Organic and biorganic chemistry, they also accept computational stuff Journal Bioorganic chemistry Journal of structural chemistry Best wishes Mahmoud http://people.bath.ac.uk/mess20/ On 5/16/11 9:44 AM, Andreas Uhe andreas.uhe{}rwth-aachen.de wrote: > > Sent to CCL by: Andreas Uhe [andreas.uhe|*|rwth-aachen.de] > Dear Kimshu, > > the Journal of Computational Chemistry (JCC) and the Journal of > Chemical Theory and Computation (JCTC) are further options. > Computational works are also accepted for publication in Chemistry - A > European Journal. > > Kind regards, > Andi > > > > Am 16.05.2011 05:16, schrieb kimshu kanmo kimshukanmo[#]gmail.com: >> Sent to CCL by: "kimshu kanmo" [kimshukanmo^gmail.com] >> Hi Group, >> please help me in knowing the names of journals (besides established >> journals >> such as JPCA,JCP,PCCP,angew chem, JACS, IJQC, Theom.Chem. Acc) in which >> computational work can be published. >> >> thanks. >> kimshu >> koreahttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > From owner-chemistry@ccl.net Mon May 16 15:16:01 2011 From: "i.nick]*[mail.ru" To: CCL Subject: CCL:G: Chemissian Message-Id: <-44661-110516102102-28687-cfNunDyeOOBGX50MQad+mQ_+_server.ccl.net> X-Original-From: i.nick!A!mail.ru Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1251 Date: Mon, 16 May 2011 18:20:15 +0400 MIME-Version: 1.0 Sent to CCL by: i.nick],[mail.ru Hello Ulrike, I recently made such plots easily, but between neutral and cation species, so I got Fukui functions. I suggest you to use gaussview, create cub files with ED and then subtract them. Âû ïèñàëè 16 ìàÿ 2011 ã., 10:39:42: > Sent to CCL by: Ulrike Salzner [salzner[*]fen.bilkent.edu.tr] > Hello, > I have downloaded the trial version of "Chemissian" to plot electron > density differences between anions and neutral species from G09 > calculations. I am using the gfinput, p and pop=full keywords. Upon > opening the files I get a window saying "error reading basis set". I > tried also G03 to see whether there is a version problem. Did not work > either. Does anyone know how to get around this or is there any other > program for Windows or LINUX that can do such plots? > Thank in advance, > Ulrike -- Ñ óâàæåíèåì, i mailto:i.nick^mail.ru From owner-chemistry@ccl.net Mon May 16 15:51:00 2011 From: "David A Mannock dmannock%x%ualberta.ca" To: CCL Subject: CCL: Chemoinformatics Message-Id: <-44662-110516150055-16636-n27gLqdisGfbGe+aPpAM5Q*o*server.ccl.net> X-Original-From: David A Mannock Content-Type: multipart/alternative; boundary=bcaec50163472462fb04a36945d3 Date: Mon, 16 May 2011 13:00:33 -0600 MIME-Version: 1.0 Sent to CCL by: David A Mannock [dmannock%ualberta.ca] --bcaec50163472462fb04a36945d3 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable That's good. A table of contents does help people decide on whether it is worth following up on the book. These are not always available for viewing online. Dave On Mon, May 16, 2011 at 6:54 AM, David Livingstone davel a chemquestuk.com = < owner-chemistry-*-ccl.net> wrote: > > Sent to CCL by: "David Livingstone" [davel---chemquestuk.com] > Dear All, > > > Dear CCLrs, > > > > Recently my faculty is considering to offer an undergraduate course on > > Chemoinformatics, for chemistry students. Though I=B4ve been working a = bit > > on computational chemistry, I do not feel I have the proper vision to > > built up a syllabus proposal, or even for giving a reasonable criticism > of > > anyone else proposal. I would really appreciate your opinion on > > what should be included in a course of such a level? > > After the recent debate here on books and piracy which got quite heated a= t > times I'm hesitant to suggest this! > > Following numerous requests from colleagues and students to recommend a > book on statistics for quantitative drug design I wrote one myself in 199= 5. > I > revised and updated this to make it more generally applicable (and perhap= s > appeal to a wider audience?) and it was published by Wiley in 2009 (ISBN > 978-0-470-85153-1). You can see the contents on my website at > http://www.chemquestuk.com/page20a.html. > > It might be something that your students find useful and/or may be of som= e > help in structuring your course. > > Regards, > > David L > > -- > D.J. Livingstone ChemQuest > Delamere House, 1 Royal Crescent, > Sandown. Isle of Wight UK PO36 8LZ > > Phone: +44 (0)1983 406832 > e-mail davel.-*-.chemquestuk.com www.chemquestuk.com > ------------------------------------------------------------------ > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --bcaec50163472462fb04a36945d3 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable That's good. A table of contents does help people decide on whether it = is worth following up on the book. These are not always available for viewi= ng online. Dave

On Mon, May 16, 2011 at 6= :54 AM, David Livingstone davel a chemqu= estuk.com <owner-chemistry-*-ccl.net> wrote:

Sent to CCL by: "David Livingstone" [davel---chemquestuk.com]
Dear All,

> Dear CCLrs,
> =A0
> Recently my faculty is considering to offer an undergraduate course on=
> Chemoinformatics, for chemistry students. Though I=B4ve been working a= bit
> on computational chemistry, I do not feel I have the proper vision=A0t= o
> built up a syllabus proposal, or even=A0for giving a reasonable=A0crit= icism of
> anyone else proposal. =A0 I would really appreciate your opinion on > what=A0should be included in a course of such a level?

After the recent debate here on books and piracy which got quite heated at<= br> times I'm hesitant to suggest this!

Following numerous requests from colleagues and students to recommend a
book on statistics for quantitative drug design I wrote one myself in 1995.= I
revised and updated this to make it more generally applicable (and perhaps<= br> appeal to a wider audience?) and it was published by Wiley in 2009 (ISBN 978-0-470-85153-1). You can see the contents on my website at
http:= //www.chemquestuk.com/page20a.html.

It might be something that your students find useful and/or may be of some<= br> help in structuring your course.

Regards,

David L

--
D.J. Livingstone =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0ChemQuest
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Delamere House, 1 Royal Cresce= nt,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Sandown. Isle of Wight UK PO36= 8LZ

Phone: +44 (0)1983 406832
e-mail davel.-*-.chemque= stuk.com =A0 =A0 www.chemquestuk.com
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--bcaec50163472462fb04a36945d3-- From owner-chemistry@ccl.net Mon May 16 22:15:00 2011 From: "arslan ali arslanali1986*gmail.com" To: CCL Subject: CCL: which basis set Message-Id: <-44663-110516114402-10146-HuBKPxO1fsPz0lKbSEKmDg(-)server.ccl.net> X-Original-From: arslan ali Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 16 May 2011 08:43:33 -0700 MIME-Version: 1.0 Sent to CCL by: arslan ali [arslanali1986=gmail.com] hello dear João Henriques, i am very thankfull for your valuable reply, are these basis sets "6-31G(d) (Valence Double Zeta + Polarization (Li-Ar)" also good for charged species? regards Arslan On 5/12/11, João Henriques joao.henriques.32353*gmail.com wrote: > Hi Arslan, > > Well it depends on your final objective and how accurate you want the > computation to be. This subject is non-black-box. However I would recommend > 6-31G(d) (Valence Double Zeta + Polarization (Li-Ar)). It is relatively > accurate and not that computationally expensive. Most publications in the > field use this basis set for this type of calculation on CHNO elements. > > Regards, > > On Tue, May 10, 2011 at 7:06 AM, arslan ali arslanali1986{:}gmail.com < > owner-chemistry() ccl.net> wrote: > >> hi, >> >> can anybody please tell me, which basis set in DFT will be more >> appropriate >> for geometry optimization of molecules of aprox 500 amu containing CHNO >> elements only?? >> >> thanks in advance >> >> Arslan >> > > > > -- > João Henriques, MSc in Biochemistry > Faculty of Science of the University of Lisbon > Department of Chemistry and Biochemistry > C8 Building, Room 8.5.47 > Campo Grande, 1749-016 Lisbon, Portugal > E-mail: joao.henriques.32353() gmail.com / jmhenriques() fc.ul.pt > http://intheochem.fc.ul.pt/members/joaoh.html >