From owner-chemistry@ccl.net Tue Jul 17 07:10:00 2007 From: "Kalyan chaitanya kalyanpulipaka{=}gmail.com" To: CCL Subject: CCL: docking papers and structure analysis Message-Id: <-34753-070716153140-1255-YvWiwD45C6nk6neX3ft9LQ _ server.ccl.net> X-Original-From: "Kalyan chaitanya" Content-Type: multipart/alternative; boundary="----=_Part_71827_29887959.1184610715829" Date: Tue, 17 Jul 2007 00:01:55 +0530 MIME-Version: 1.0 Sent to CCL by: "Kalyan chaitanya" [kalyanpulipaka^gmail.com] ------=_Part_71827_29887959.1184610715829 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline dear all, Can any one tell if there is any research worked published on this work- i.e . done homology modeling, predicted binding pockets and did protein-protein docking with those homology models, actually i have done the same but findng little difficult or rather confused how to put the results on paper, if any one can send me the paper or give me the reference, that will be of great help to me, also Can any one tell me if there is any server, which ld give us the information about possible hydrophobic interactions and disulphide bridges between the residues when a pdb structure is given Thank you in advance, P.Kalyan ________________________________________________ ------=_Part_71827_29887959.1184610715829 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
dear all,

Can any one tell if there is any research worked published on this work- i.e.
done homology modeling, predicted binding pockets and did protein-protein
docking with those homology models,

actually i have done the same but findng little difficult or rather
confused how to put the results on paper, if any one can send me the paper
or give me the reference, that will be of great help to me,
 
also Can any one tell me if there is any server, which ld give us the information about possible hydrophobic interactions and disulphide bridges between the residues when a pdb structure is given

Thank you in advance,

P.Kalyan
________________________________________________
------=_Part_71827_29887959.1184610715829-- From owner-chemistry@ccl.net Tue Jul 17 08:27:00 2007 From: "Shrinwantu Pal paul**jncasr.ac.in" To: CCL Subject: CCL: total energy : adf Message-Id: <-34754-070717081803-16551-K1J6JHArQCqeuyhkWBCMAQ=server.ccl.net> X-Original-From: "Shrinwantu Pal" Date: Tue, 17 Jul 2007 08:17:59 -0400 Sent to CCL by: "Shrinwantu Pal" [paul\a/jncasr.ac.in] DEAR COLLEAGUES, I DO NOT SEEM TO FIGURE OUT HOW TO USE ADF IN FINDING OUT THE TOTAL ENERGY OF A SYSTEM. I WOULD LIKE TO STRESS THAT I HAVE USED ADF TO GET INTERACTION ENERGIES BETWEEN FRAGMENTS, BUT AS IN THIS CASE I NEED THE TOTAL ENERGY. IS THERE A WAY WHERE ONE CAN DEFINE EACH ATOM AS A FRAGMENT AND CALCULATE INTERACTION ENERGY? BUT THEN THERE IS A PROBLEM ABOUT THE ATOM NOT BEING CONSIDERED PROPERLY AS THE ATOM WHILE IN BONDING, IS NO LONGER SPHERICAL. DO WE THEN CORRECT THE INTERACTION ENERGY SUPPORTED BY 'BSSE' ? ANY HELP FROM YOU ALL WOULD BE HUMBLY APPRECIATED. ~Shrinwantu Pal TSU JNCASR INDIA From owner-chemistry@ccl.net Tue Jul 17 09:02:00 2007 From: "Shrinwantu Pal paul_-_jncasr.ac.in" To: CCL Subject: CCL: singlet vs triplet Message-Id: <-34755-070717082234-17466-oatAmKE087cx0nEMscctvw..server.ccl.net> X-Original-From: "Shrinwantu Pal" Date: Tue, 17 Jul 2007 08:22:31 -0400 Sent to CCL by: "Shrinwantu Pal" [paul(!)jncasr.ac.in] Dear colleagues, If i have a metal which can exist in a singlet and a triplet state, i would be very thankful if someone lends me some light as to how: using adf i can get to know which one is going to be more stable? thanks in advance, ~Shrinwantu Pal TSU JNCASR India From owner-chemistry@ccl.net Tue Jul 17 09:37:00 2007 From: "vijayan_rs],[iicb.res.in" To: CCL Subject: CCL: computational Drug discovery seminar at IICB , Kolkata, India. Message-Id: <-34756-070717074458-3657-DVMxo+VvKt/9Yf3LRP6dkQ~~server.ccl.net> X-Original-From: vijayan_rs]=[iicb.res.in Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 17 Jul 2007 16:28:18 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: vijayan_rs*|*iicb.res.in Dear CCL members IICB Kolkata,India and Schrodinger are jointly conducting a one day symposium on Computational Drug discovery in Pharma R & D at IICB, Kolkata, campus on 3rd August 2007 Interested participants are requested to look in to the website for more details. http://www.iicb.res.in/cdd/index.html With Regards R.S.K.Vijayan Senior Research Fellow Structural Biology & Bioinformatics Division Indian Institute of Chemical Biology Kolkata -32, India From owner-chemistry@ccl.net Tue Jul 17 12:46:00 2007 From: "Dhurairaj Senthilnathan zenthil03_._yahoo.co.in" To: CCL Subject: CCL: total energy : adf Message-Id: <-34757-070717123932-22524-JtNA8j9XeB1A/V7pffb/hA- -server.ccl.net> X-Original-From: Dhurairaj Senthilnathan Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1156912268-1184690343=:16596" Date: Tue, 17 Jul 2007 17:39:03 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Dhurairaj Senthilnathan [zenthil03%x%yahoo.co.in] --0-1156912268-1184690343=:16596 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear Shrinwantu Pal, There is no way to directly find out the total energy values of particular chemical system in ADF. ADF output only print the total bonding energy of particular system through bonding energy decomposition analysis. But some indirect way is there for energy calculation E.x. Etot = Epauli + Eorb + Eelstat If you need more explanation you can cite Prof. Gernot Frenking reviews and publications. It will help you thank you senthilnathan "Shrinwantu Pal paul**jncasr.ac.in" wrote: Sent to CCL by: "Shrinwantu Pal" [paul\a/jncasr.ac.in] DEAR COLLEAGUES, I DO NOT SEEM TO FIGURE OUT HOW TO USE ADF IN FINDING OUT THE TOTAL ENERGY OF A SYSTEM. I WOULD LIKE TO STRESS THAT I HAVE USED ADF TO GET INTERACTION ENERGIES BETWEEN FRAGMENTS, BUT AS IN THIS CASE I NEED THE TOTAL ENERGY. IS THERE A WAY WHERE ONE CAN DEFINE EACH ATOM AS A FRAGMENT AND CALCULATE INTERACTION ENERGY? BUT THEN THERE IS A PROBLEM ABOUT THE ATOM NOT BEING CONSIDERED PROPERLY AS THE ATOM WHILE IN BONDING, IS NO LONGER SPHERICAL. DO WE THEN CORRECT THE INTERACTION ENERGY SUPPORTED BY 'BSSE' ? ANY HELP FROM YOU ALL WOULD BE HUMBLY APPRECIATED. ~Shrinwantu Pal TSU JNCASR INDIAhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt________________________________________________________________________ Mr.D.SENTHILNATHAN , Research Scholar, School of Chemistry, Bharathidasan University, TIRUCHIRAPPALLI - 620 024, TamilNadu, INDIA http://chemthilchem.googlepages.com/whoiami Phone : + 91 431 2407053(office) + 94 437 81355 (Mobile) E-mail: zenthil03%%yahoo.co.in chemthilchem%%gmail.com --------------------------------- Why delete messages? Unlimited storage is just a click away. --0-1156912268-1184690343=:16596 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Dear Shrinwantu Pal,
                            There is no way to directly  find out the total energy values of particular chemical system in ADF. ADF output only print the total bonding energy of particular system through bonding energy decomposition analysis. But some indirect way is there for energy calculation
               E.x. Etot = Epauli + Eorb + Eelstat
If you need more explanation you can cite Prof. Gernot Frenking reviews and publications. It will help you
 
thank you
senthilnathan
 
 
"Shrinwantu Pal paul**jncasr.ac.in" <owner-chemistry%%ccl.net> wrote:

Sent to CCL by: "Shrinwantu Pal" [paul\a/jncasr.ac.in]
DEAR COLLEAGUES,

I DO NOT SEEM TO FIGURE OUT HOW TO USE ADF IN FINDING OUT THE TOTAL ENERGY OF A SYSTEM.

I WOULD LIKE TO STRESS THAT I HAVE USED ADF TO GET INTERACTION ENERGIES BETWEEN FRAGMENTS, BUT AS IN THIS CASE I NEED THE TOTAL ENERGY.

IS THERE A WAY WHERE ONE CAN DEFINE EACH ATOM AS A FRAGMENT AND CALCULATE INTERACTION ENERGY?

BUT THEN THERE IS A PROBLEM ABOUT THE ATOM NOT BEING CONSIDERED PROPERLY AS THE ATOM WHILE IN BONDING, IS NO LONGER SPHERICAL.

DO WE THEN CORRECT THE INTERACTION ENERGY SUPPORTED BY 'BSSE' ?

ANY HELP FROM YOU ALL WOULD BE HUMBLY APPRECIATED.

~Shrinwantu Pal
TSU
JNCASR
INDIA


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________________________________________________________________________

Mr.D.SENTHILNATHAN ,
Research Scholar,
School of Chemistry,
Bharathidasan University,
TIRUCHIRAPPALLI - 620 024,
TamilNadu, INDIA
http://chemthilchem.googlepages.com/whoiami

Phone : + 91 431 2407053(office)
+ 94 437 81355 (Mobile)

E-mail: zenthil03%%yahoo.co.in
chemthilchem%%gmail.com

Why delete messages? Unlimited storage is just a click away. --0-1156912268-1184690343=:16596-- From owner-chemistry@ccl.net Tue Jul 17 13:36:00 2007 From: "Rachel Crespo Otero rachel{=}fq.uh.cu" To: CCL Subject: CCL: SAPT to open shell systems Message-Id: <-34758-070717131118-2990-klFS503TC2zzpfYVLbewHQ!=!server.ccl.net> X-Original-From: Rachel Crespo Otero Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Tue, 17 Jul 2007 12:12:44 -0400 (CDT) MIME-Version: 1.0 Sent to CCL by: Rachel Crespo Otero [rachel*_*fq.uh.cu] Dear CCL members, Anybody knows a program based on SAPT (Symmetry-Adapted Perturbation Theory) that can be applied to open shell intermolecular complexes? Best regards, Rachel