From owner-chemistry@ccl.net Fri Jun 23 07:11:00 2017 From: "Manish Kumar Gupta mkgupta5-,-gmail.com" To: CCL Subject: CCL: To calculate ligand binding site in VINA Message-Id: <-52862-170623070821-13357-qb1yJAWj7Rhgb94hGf3L3w * server.ccl.net> X-Original-From: "Manish Kumar Gupta" Date: Fri, 23 Jun 2017 07:08:19 -0400 Sent to CCL by: "Manish Kumar Gupta" [mkgupta5 * gmail.com] Hi I am working of Ligand-Receptor docking using VINA. How to define binding site coordinates in VINA. Previously, I was using GOLD which uses straightforward approaches like Ligand/ a central point/residue list to define the binding site. Please reply Manish From owner-chemistry@ccl.net Fri Jun 23 09:22:00 2017 From: "Elvis Martis elvis_bcp+/-elvismartis.in" To: CCL Subject: CCL: To calculate ligand binding site in VINA Message-Id: <-52863-170623091325-19033-BWgncStG3u07qUpEgD9QCQ,server.ccl.net> X-Original-From: Elvis Martis Content-Type: multipart/alternative; boundary="94eb2c1aba781ecc380552a05dc9" Date: Fri, 23 Jun 2017 18:42:53 +0530 MIME-Version: 1.0 Sent to CCL by: Elvis Martis [elvis_bcp(0)elvismartis.in] --94eb2c1aba781ecc380552a05dc9 Content-Type: text/plain; charset="UTF-8" HI, First of all load your protein-ligand complex in MGL-Tools. Since your ligand is bound, you can ask MGL-Tools to centre the GRID centre to the centre of Mass of the ligand. Note the X,Y,Z coordinates and the box dimensions. This will be your binding site for VINA which you need to enter in the config file. Best Regards [image: photo] Elvis Martis Ph.D. Student (Computational Chemistry) at Bombay College of Pharmacy A Kalina, Santacruz [E], Mumbai 400098, INDIA W www.elvismartis.in Skype. adrian_elvis12 On 23 June 2017 at 16:38, Manish Kumar Gupta mkgupta5-,-gmail.com < owner-chemistry]^[ccl.net> wrote: > > Sent to CCL by: "Manish Kumar Gupta" [mkgupta5 * gmail.com] > Hi > I am working of Ligand-Receptor docking using VINA. > How to define binding site coordinates in VINA. > > > > Previously, I was using GOLD which uses straightforward approaches like > Ligand/ > a central point/residue list to define the binding site. > > Please reply > > Manish> > > --94eb2c1aba781ecc380552a05dc9 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
HI,
First of all load your protein-ligand complex i= n MGL-Tools.
Since your ligand is bound, you can ask MGL-Tools to cen= tre the GRID centre to the centre of Mass of the ligand. Note the X,Y,Z coo= rdinates and the box dimensions.
This will be your binding site for V= INA which you need to enter in the config file.


=
=C2=A0 =C2= =A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Best Regards
3D"photo"

Elvis Martis
Ph.D. Student (Computational Chemistry)
=C2= =A0at=C2=A0Bombay College of Pharmacy
A=C2=A0=C2= =A0Kalina, Santacruz [E], Mumbai 400098, INDIA
W=C2=A0= www.elvismartis.inSkype.=C2=A0adrian_elvis1= 2


On 23 June 2017 at 16:38, Manish Kumar Gupta= mkgupta5-,-gmail.com &l= t;owner-chemis= try]^[ccl.net> wrote:

Sent to CCL by: "Manish Kumar=C2=A0 Gupta" [mkgupta5 * gmail.com]
Hi
I am working of Ligand-Receptor docking using VINA.
How to define binding site coordinates in VINA.



Previously, I was using GOLD which uses straightforward approaches like Lig= and/
a central point/residue list to define the binding site.

Please reply

Manish



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