From owner-chemistry@ccl.net Wed Feb 23 08:06:01 2011 From: "Jorge Echeverria jorge.echeverria..qi.ub.es" To: CCL Subject: CCL:G: Elecron density at a given point with Gaussian Message-Id: <-44003-110223051408-28222-yFD6jXmKhfYJKgSZJN2kHg]~[server.ccl.net> X-Original-From: "Jorge Echeverria" Date: Wed, 23 Feb 2011 05:14:07 -0500 Sent to CCL by: "Jorge Echeverria" [jorge.echeverria!^!qi.ub.es] Dear users, I would like to know the value of the electron density at an arbitary point of a molecule, not on a bond or a critical point after a MP2 calculation. Is it possible to do it by generating a cube file with Gaussian? Maybe with a AIM analysis software? Any help will be very welcome, Jorge Echeverria. From owner-chemistry@ccl.net Wed Feb 23 11:35:00 2011 From: "ABHISHEK SHAHI shahi.abhishek1984 ~~ gmail.com" To: CCL Subject: CCL:G: Elecron density at a given point with Gaussian Message-Id: <-44004-110223111233-29529-IGv/jyO1Umf6iAyun5RAnQ(!)server.ccl.net> X-Original-From: ABHISHEK SHAHI Content-Type: multipart/alternative; boundary=0016364d1ca5c800e4049cf55c1a Date: Wed, 23 Feb 2011 21:42:24 +0530 MIME-Version: 1.0 Sent to CCL by: ABHISHEK SHAHI [shahi.abhishek1984|a|gmail.com] --0016364d1ca5c800e4049cf55c1a Content-Type: text/plain; charset=ISO-8859-1 Dear Jorge Echeverria, AIM2000 can help you. Follow the following step.... 1. open aim2000(freeware Bader's Page) 2. load your molecule(use .wfn file) 3. calculate >> Properties of density function 4. In co-ordinate box, give your point(x,y,z) where you want to calculate the electron density. 5. click on calculate. Hope this will help you. With regards; *ABHISHEK SHAHI* *Research Scholar Inorganic and Physical Chemistry Indian Institute Of Science Bangalore-12* On Wed, Feb 23, 2011 at 3:44 PM, Jorge Echeverria jorge.echeverria..qi.ub.es wrote: > > Sent to CCL by: "Jorge Echeverria" [jorge.echeverria!^!qi.ub.es] > Dear users, > > I would like to know the value of the electron density at an arbitary point > of a molecule, not on a bond > or a critical point after a MP2 calculation. Is it possible to do it by > generating a cube file with > Gaussian? Maybe with a AIM analysis software? > Any help will be very welcome, > > Jorge Echeverria.> > > --0016364d1ca5c800e4049cf55c1a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Jorge Echeverria,

=A0=A0=A0 AIM2000 can help you. Follow the f= ollowing step....

  1. open aim2000(freeware Bader's Page)
  2. load your molecule(use .wfn file)
  3. calculate >> Prop= erties of density function
  4. In co-ordinate box, give your point(x,y,z) where you want to calculate = the electron density.
  5. click on calculate.
Hope this will h= elp you.



With regards;
=A0ABHISHEK SHAHI

Research Scholar
In= organic and Physical Chemistry
Indian Institute Of Science
Ba= ngalore-12



On Wed, Feb 23, 2011 at 3:44 PM, Jorge E= cheverria jorge.echeverria..qi.ub.es <owner-chemistry(!)= ccl.net> wrote:

Sent to CCL by: "Jorge =A0Echeverria" [jorge.echeverria!^!qi.ub.es]
Dear users,

I would like to know the value of the electron density at an arbitary point= of a molecule, not on a bond
or a critical point after a MP2 calculation. Is it possible to do it by gen= erating a cube file with
Gaussian? Maybe with a AIM analysis software?
Any help will be very welcome,

Jorge Echeverria.



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--0016364d1ca5c800e4049cf55c1a-- From owner-chemistry@ccl.net Wed Feb 23 13:30:00 2011 From: "sadia zafar diya.khan.05]=[gmail.com" To: CCL Subject: CCL: binding of ligand on protein in water box Message-Id: <-44005-110223120206-28643-8qW4va+Oe/qbU1MzDUodJw-$-server.ccl.net> X-Original-From: sadia zafar Content-Type: multipart/alternative; boundary=000e0ce0b206275b46049cf60e42 Date: Wed, 23 Feb 2011 22:02:00 +0500 MIME-Version: 1.0 Sent to CCL by: sadia zafar [diya.khan.05[*]gmail.com] --000e0ce0b206275b46049cf60e42 Content-Type: text/plain; charset=ISO-8859-1 Respected Sir! I want to add a ligand molecule (sugar chain) on my protein. I have been searching for its procedure in the archive of the NAMD mailing lists and also on the web but could not find methodology. Can you please guide me that how I can perform protein-ligand simulation? Secondly is it better to take a start by initially adding the ligand to the protein structure i.e. making a protein-ligand complex and then running simulations on it or should I do simulation of the protein alone and then do the addition of ligand molecule? Thanks. --000e0ce0b206275b46049cf60e42 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Respected Sir!
=A0=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 I want to= add a ligand molecule (sugar chain) on my protein. I have been searching f= or its procedure in the archive of the NAMD mailing lists and also on the w= eb but could not find methodology.
Can you please guide me that how I can perform protein-ligand simulati= on?=A0
Secondly is it better to take a start by initially adding = the ligand to the protein structure i.e. making a protein-ligand complex an= d then running simulations on it or should I do simulation of the protein a= lone and then do the addition of ligand molecule?

Thanks.
--000e0ce0b206275b46049cf60e42-- From owner-chemistry@ccl.net Wed Feb 23 14:57:00 2011 From: "amirhossein taghavi taghavi.amirhossein-x-gmail.com" To: CCL Subject: CCL: binding of ligand on protein in water box Message-Id: <-44006-110223144237-614-G/VisG/sJND+LMVV8488qQ() server.ccl.net> X-Original-From: amirhossein taghavi Content-Type: multipart/alternative; boundary=e0cb4e6ff3653a78bf049cf84cea Date: Wed, 23 Feb 2011 23:12:31 +0330 MIME-Version: 1.0 Sent to CCL by: amirhossein taghavi [taghavi.amirhossein(~)gmail.com] --e0cb4e6ff3653a78bf049cf84cea Content-Type: text/plain; charset=ISO-8859-1 Dear Sadia, there is an advanced Amber tutorial for setting up a system for DNA ligand interaction it may help you for setting up your system http://ambermd.org/tutorials/advanced/tutorial1/ good luck On Wed, Feb 23, 2011 at 8:32 PM, sadia zafar diya.khan.05]=[gmail.com < owner-chemistry a ccl.net> wrote: > Respected Sir! > I want to add a ligand molecule (sugar chain) on my > protein. I have been searching for its procedure in the archive of the NAMD > mailing lists and also on the web but could not find methodology. > Can you please guide me that how I can perform protein-ligand simulation? > Secondly is it better to take a start by initially adding the ligand to the > protein structure i.e. making a protein-ligand complex and then running > simulations on it or should I do simulation of the protein alone and then do > the addition of ligand molecule? > > Thanks. > --e0cb4e6ff3653a78bf049cf84cea Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Sadia,

there is an advanced Amber tutorial for setting up a sys= tem for DNA ligand interaction it may help you for setting up your systemhttp://amber= md.org/tutorials/advanced/tutorial1/

good luck

On Wed, Feb 23, 2011 at 8:= 32 PM, sadia zafar diya.khan.05]=3D[gmail.com<= /a> <owner-= chemistry a ccl.net> wrote:
Respected Sir!=A0=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 I want to add a ligand mol= ecule (sugar chain) on my protein. I have been searching for its procedure = in the archive of the NAMD mailing lists and also on the web but could not = find methodology.
Can you please guide me that how I can perform protein-ligand simulati= on?=A0
Secondly is it better to take a start by initially adding = the ligand to the protein structure i.e. making a protein-ligand complex an= d then running simulations on it or should I do simulation of the protein a= lone and then do the addition of ligand molecule?

Thanks.

--e0cb4e6ff3653a78bf049cf84cea-- From owner-chemistry@ccl.net Wed Feb 23 20:43:00 2011 From: "Chenghua Zhang zchua126.com[*]126.com" To: CCL Subject: CCL: binding of ligand on protein in water box Message-Id: <-44007-110223201617-15936-8OAaa+dQT0difPikYxssVg,+,server.ccl.net> X-Original-From: "Chenghua Zhang" Content-Type: multipart/alternative; boundary="----=_Part_203201_735640320.1298510155232" Date: Thu, 24 Feb 2011 09:15:55 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: "Chenghua Zhang" [zchua126.com-*-126.com] ------=_Part_203201_735640320.1298510155232 Content-Type: text/plain; charset=GBK Content-Transfer-Encoding: 7bit 1. dock the lignad to the active site of the protein using autodock4.2, you could obtain the ES complex 2. add waters and MD -- Sincerely Chenghua Zhang College of Chemistry Sichuan University, China. ------=_Part_203201_735640320.1298510155232 Content-Type: text/html; charset=GBK Content-Transfer-Encoding: 7bit
1. dock the lignad to the active site of the protein using autodock4.2, you could obtain the ES complex
2. add waters and MD
--
Sincerely
Chenghua Zhang
College of Chemistry
Sichuan University, China.



------=_Part_203201_735640320.1298510155232-- From owner-chemistry@ccl.net Wed Feb 23 23:15:00 2011 From: "Rajan Chaudhari rchaudhari%x%mail.usp.edu" To: CCL Subject: CCL: binding of ligand on protein in water box Message-Id: <-44008-110223144707-4313-v7BNGxGL3Ap5YFxaW15iGQ],[server.ccl.net> X-Original-From: Rajan Chaudhari Content-Type: multipart/alternative; boundary="_e4979968-43cd-44fc-9fa1-1d7bfc5d30e9_" Date: Wed, 23 Feb 2011 14:46:59 -0500 MIME-Version: 1.0 Sent to CCL by: Rajan Chaudhari [rchaudhari(a)mail.usp.edu] --_e4979968-43cd-44fc-9fa1-1d7bfc5d30e9_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello Zafer=2C You need to perform docking experiments first. It will give you binding mod= e of the ligand. You can look for softwares like Autodock (Freeware)=2C FRE= D=2C Flexidock=2C Glide=2C and GOLD. After this you might be interested in = performing molecular dynamics simulations using GROMACS(Freeware)=2C Desmon= d or similar softwares available to you. Read the manuals and related paper= s. Best Luck! Regards=2CRajan > From: owner-chemistry .. ccl.net To: rchaudhari .. mail.usp.edu Subject: CCL: binding of ligand on protein in water box Date: Wed=2C 23 Feb 2011 22:02:00 +0500 Respected Sir! I want to add a ligand molecule (sugar= chain) on my protein. I have been searching for its procedure in the archi= ve of the NAMD mailing lists and also on the web but could not find methodo= logy. Can you please guide me that how I can perform protein-ligand simulation? S= econdly is it better to take a start by initially adding the ligand to the = protein structure i.e. making a protein-ligand complex and then running sim= ulations on it or should I do simulation of the protein alone and then do t= he addition of ligand molecule? Thanks. = --_e4979968-43cd-44fc-9fa1-1d7bfc5d30e9_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello Zafer=2C

You need to perform docking experiments f= irst. It will give you binding mode of the ligand. You can look for softwar= es like Autodock (Freeware)=2C FRED=2C Flexidock=2C Glide=2C and GOLD. Afte= r this you might be interested in performing molecular dynamics simulations= using GROMACS(Freeware)=2C Desmond or similar softwares available to you. = Read the manuals and related papers.

Best Luck!

Regards=2C
Rajan

=
From: owner-chemistry .. ccl.net
To: rchaudhari .. mai= l.usp.edu
Subject: CCL: binding of ligand on protein in water box
Dat= e: Wed=2C 23 Feb 2011 22:02:00 +0500

Respected Sir!
 =3B&nbs= p=3B  =3B  =3B  =3B  =3B  =3B  =3B  =3B  = =3B  =3B  =3B I want to add a ligand molecule (sugar chain) on my p= rotein. I have been searching for its procedure in the archive of the NAMD = mailing lists and also on the web but could not find methodology.
Can you please guide me that how I can perform protein-ligand simulati= on? =3B
Secondly is it better to take a start by initially ad= ding the ligand to the protein structure i.e. making a protein-ligand compl= ex and then running simulations on it or should I do simulation of the prot= ein alone and then do the addition of ligand molecule?

Thanks.
= --_e4979968-43cd-44fc-9fa1-1d7bfc5d30e9_--