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.

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