From owner-chemistry@ccl.net Tue Jul 12 00:22:00 2011 From: "neeraj misra neerajmisra=-=hotmail.com" To: CCL Subject: CCL: CNT and Biomoelcule Message-Id: <-45064-110712002037-21520-oGuO15V1E9bplrR8YGqk2Q]=[server.ccl.net> X-Original-From: "neeraj misra" Date: Tue, 12 Jul 2011 00:20:34 -0400 Sent to CCL by: "neeraj misra" [neerajmisra..hotmail.com] Dear members, I wish to study the interaction of a CNT with drug molecule and for this i am not too sure about how to approach. Do I need to carry out a MD simulation to know the site of interaction and the model the two systems for further studies or else. Please post your suggestions/advice for this querry.Is there any free code avialble for MD simulation studies? Thanks in advance NM From owner-chemistry@ccl.net Tue Jul 12 02:20:00 2011 From: "psavita=-=crlindia.com" To: CCL Subject: CCL: CNT and Biomoelcule Message-Id: <-45065-110712021026-22546-Bw9Br3iXAAGREqr1YPDRUg%server.ccl.net> X-Original-From: psavita/a\crlindia.com Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Date: Tue, 12 Jul 2011 11:45:06 +0530 MIME-Version: 1.0 MIME-Version: 1.0 Sent to CCL by: psavita]~[crlindia.com
Hello Neeraj,

In my view, you could first perform dockin= g using standard available tools such as Autodock and then go for
MD to = check the stability of docked structure. Gromacs, NwChem, LAMMPS are some o= f the MD freeware tools.

Best wishes,

= Savita PundlikComputati= onal Materials Applied Researc= h 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, Savita Sunil " <psavita=crlindia.com>
From: "nee= raj misra neerajmisra=3D-=3Dhotmail.com" <owner-chemistry=ccl.net>
Sent by:
owner-chemistry+psavita=3D=3Dcrl= india.com=ccl.net
Date: 07/12/2011 09:50AM
Subject: CCL: CNT and = Biomoelcule

=
Sent to CCL by: "neeraj  misra" [neerajmisra..hotmail.com]
Dear= members,
                I= wish to study the interaction of a CNT with drug molecule and for this i a= m not too sure about how to approach. Do I need to carry out a MD simulatio= n to know the site of interaction and the  model the two systems for f= urther studies or else. Please post your suggestions/advice for this querry= .Is there any free code avialble for MD simulation studies?
Thanks in ad= vance
NM



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= From owner-chemistry@ccl.net Tue Jul 12 08:11:00 2011 From: "ela guru - gsmaran07.(0).rediffmail.com" To: CCL Subject: CCL: Visualize absorption spectra Message-Id: <-45066-110712043423-20281-gtvYJwapujSrFo5NB0D/7w(0)server.ccl.net> X-Original-From: "ela guru -" Date: Tue, 12 Jul 2011 04:34:21 -0400 Sent to CCL by: "ela guru -" [gsmaran07|a|rediffmail.com] Dear ccl members, How to visualize absorption spectra from TDDFT output . Is there any software available? And could you suggest a possible software to merge experimental UV-spectra with theoretical UV-spectra? You help will be appreciate Thanks in advance ELA From owner-chemistry@ccl.net Tue Jul 12 09:55:01 2011 From: "Geoffrey Hutchison geoffh^pitt.edu" To: CCL Subject: CCL: Visualize absorption spectra Message-Id: <-45067-110712095200-3514-8MzMIlREH3k/lgHp7S+nCA,,server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=us-ascii Date: Tue, 12 Jul 2011 09:51:50 -0400 MIME-version: 1.0 (Apple Message framework v1084) Sent to CCL by: Geoffrey Hutchison [geoffh ~~ pitt.edu] > How to visualize absorption spectra from TDDFT output . Is there any software available? > And could you suggest a possible software to merge experimental UV-spectra with theoretical UV-spectra? Avogadro can do both of these. http://avogadro.sf.net/ Best regards, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh%%pitt.edu web: http://hutchison.chem.pitt.edu/ From owner-chemistry@ccl.net Tue Jul 12 10:37:00 2011 From: "Kacper Druzbicki kacper.druzbicki!=!uj.edu.pl" To: CCL Subject: CCL: Visualize absorption spectra Message-Id: <-45068-110712101922-9892-lDls7mi3bYSeIK4EXavV2A[*]server.ccl.net> X-Original-From: "Kacper Druzbicki" Date: Tue, 12 Jul 2011 10:19:09 -0400 Sent to CCL by: "Kacper Druzbicki" [kacper.druzbicki%%uj.edu.pl] Dear Ela, There are plenty of tools out there that help you to visualize the results. Some freely available ones are: http://www.chemissian.com/ (Propably the best choice for you and the most powerfull tool in this matter) You can also check http://gausssum.sourceforge.net/GaussSum2.0/index.html http://www.sg-chem.net/swizard/#download Regards, Kacper > "ela guru - gsmaran07.(0).rediffmail.com" wrote: > > Sent to CCL by: "ela guru -" [gsmaran07|a|rediffmail.com] > Dear ccl members, > > How to visualize absorption spectra from TDDFT output . Is there any software available? > > And could you suggest a possible software to merge experimental UV-spectra with theoretical UV-spectra? > > You help will be appreciate > > Thanks in advance > > ELA > > From owner-chemistry@ccl.net Tue Jul 12 11:19:00 2011 From: "Vijay Solomon vijaysolomon_2005 . yahoo.co.in" To: CCL Subject: CCL: How to identify ICT in TDDFT calculations Message-Id: <-45069-110712012828-31567-lojTyWBmB8MISMWxaLh6Ug~!~server.ccl.net> X-Original-From: Vijay Solomon Content-Type: multipart/alternative; boundary="0-1501439416-1310448498=:30331" Date: Tue, 12 Jul 2011 10:58:18 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: Vijay Solomon [vijaysolomon_2005!^!yahoo.co.in] --0-1501439416-1310448498=:30331 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable dear Jun Zhang,=0A=0A thanks a lot for your answer.=0A=0A= with regards,=0A=0Avijay =0A=0A =0A=0A________________________________=0AFr= om: Jun Zhang coolrainbow=3D-=3Dyahoo.cn =0ATo: "S= olomon, Vijay " =0ASent: Tue, 12 Jul= y, 2011 5:16:35 AM=0ASubject: CCL: How to identify ICT in TDDFT calculation= s=0A=0A=0AHello vijay:=0A =0AA simple way is to draw the molecular orbitals= and see if the orbitals involved =0Ain the excitation is spatially separat= ed within the molecule.=0A =0A=0ACheers up!=0A =0A-------------------------= ---------------------------------------=0AJun Zhang (coolrainbow^yahoo.ch)= =0AComputational Chemistry Group=0ANo.94, Weijinlu=0ANankai University =0AT= ianjin, China=0A=0A=E5=8F=91=E4=BB=B6=E4=BA=BA=EF=BC=9A vijay solomon vijay= solomon_2005[a]yahoo.co.in =0A=E6=94=B6=E4=BB=B6= =E4=BA=BA=EF=BC=9A "Zhang, Jun " =0A=E5=8F=91=E9=80= =81=E6=97=A5=E6=9C=9F=EF=BC=9A 2011=E5=B9=B47=E6=9C=8812=E6=97=A5, =E6=98= =9F=E6=9C=9F=E4=BA=8C, =E4=B8=8A=E5=8D=88 12:56=0A=E4=B8=BB=E9=A2=98: CCL: = How to identify ICT in TDDFT calculations=0A=0A=0ASent to CCL by: "vijay s= olomon" [vijaysolomon_2005[a]yahoo.co.in]=0ADear cclrs,=0A=0A In m= any papers, people used to report the intramolecular charge =0Atransfer (IC= T)for the organic molecules from TDDFT calculations or just look =0Ainto th= e HOMO/LUMO pictures of DFT outputs. what is the correct way of assigning = =0Athe ICT from DFT/TDDFT output. Is there any rule of thumb available? or = any =0Atutorial or any important papers?=0A=0Athanks in advance.=0A=0Ayour= s =0A=0Avijay=0A=0A=0A=0A-=3D This is automatically added to each message b= y the mailing script =3D-=0ATo recover the email address of the author of t= he message, please change=0A=0AE-mail to subscribers: CHEMISTRY^ccl.net or = use:=0A=0A=0AE-mail to= administrators: CHEMISTRY-REQUEST^ccl.net or use=0A http://www.ccl.ne= t/cgi-bin/ccl/send_ccl_message=0A=0A=0A http://= www.ccl.net/chemistry/sub_unsub.shtml=0A=0ABefore posting, check wait time = at: http://www.ccl.net=0A=0A=0AConferences: ht= tp://server.ccl.net/chemistry/announcements/conferences/=0A=0ASearch Messag= es: http://www.ccl.net/chemistry/searchccl/index.shtml=0A=0A http://ww= w.ccl.net/spammers.txt=0A=0ARTFI: http://www.ccl.net/chemistry/aboutccl/ins= tructions/ --0-1501439416-1310448498=:30331 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
dear Jun Zhang,

     = ;              thanks a lot for your ans= wer.

with regards,

vijay&= nbsp;

 

From: Jun Zhang coolra= inbow=3D-=3Dyahoo.cn <owner-chemistry*o*ccl.net>
To: "Solomon, Vijay " <vijaysolomon_2005*o*yaho= o.co.in>
Sent: Tue, = 12 July, 2011 5:16:35 AM
Subject:<= /span> CCL: How to identify ICT in TDDFT calculations

Hello vijay:
 
A simple way is to draw the molecular orbitals and see if the orbit= als involved in the excitation is spatially separated within the molecule.<= /div>
 

Cheers up!
 
------= ----------------------------------------------------------
Jun Zhang (co= olrainbow^yahoo.ch)
Computational Chemistry Group
No.94, Weijinlu
= Nankai University
Tianjin, China
=E5=8F=91=E4=BB= =B6=E4=BA=BA=EF=BC=9A vijay solomon vijaysolomon_2005[a]yahoo.co= .in <owner-chemistry^ccl.net>
=E6=94=B6=E4=BB=B6=E4=BA=BA=EF=BC=9A "Zhang, Jun " <coolrain= bow^yahoo.cn>
=E5=8F=91=E9=80=81= =E6=97=A5=E6=9C=9F=EF=BC=9A 2011=E5=B9=B47=E6=9C=8812=E6=97=A5, = =E6=98=9F=E6=9C=9F=E4=BA=8C, =E4=B8=8A=E5=8D=88 12:56
=E4=B8=BB=E9=A2=98: CCL: How to identify ICT = in TDDFT calculations


Sent to CCL by: "vijay  solomo= n" [vijaysolomon_2005[a]yahoo.co.in]
Dear cclrs,

    &n= bsp;     In many papers, people used to report the intramolecular= charge transfer (ICT)for the organic molecules from TDDFT calculations or just look into the HOMO/LUMO pictures of DFT outputs. what is the correct = way of assigning the ICT from DFT/TDDFT output. Is there any rule of thumb = available? or any tutorial or any important=0A papers?

thanks in adv= ance.

yours

vijay



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<= /div>
= =0A=0A=0A
--0-1501439416-1310448498=:30331-- From owner-chemistry@ccl.net Tue Jul 12 12:44:00 2011 From: "Allouche Abdul-rahman allouche]![lasim.univ-lyon1.fr" To: CCL Subject: CCL: Visualize absorption spectra Message-Id: <-45070-110712121535-23039-rj5zPdTk2MIxX34XXBHuwg- -server.ccl.net> X-Original-From: Allouche Abdul-rahman Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 12 Jul 2011 18:14:37 +0200 MIME-Version: 1.0 Sent to CCL by: Allouche Abdul-rahman [allouche|,|lasim.univ-lyon1.fr] Hello, Try Gabedit : gabedit.sourceforge.net Best regards, > Sent to CCL by: "ela guru -" [gsmaran07|a|rediffmail.com] > Dear ccl members, > > How to visualize absorption spectra from TDDFT output . Is there any software available? > > And could you suggest a possible software to merge experimental UV-spectra with theoretical UV-spectra? > > You help will be appreciate > > Thanks in advance > > ELA> > > -- Abdul-Rahman ALLOUCHE Fax : + (33) (0) 472431507 Email : allouche ~~ lasim.univ-lyon1.fr Web : http://sites.google.com/site/allouchear/