How to move a ligand

Hi, 

Here is my question. Now, I have a protein structure with a bound ligand, say ligand A. I also have another ligand (ligand B), which is in a separate file, and would like to overlay it on the top of ligand A to view its spacial arrangement. 

What I have done so far is: open the the protein structure (pdb file) and Added ligand B. When I try to translate or rotate it to the position of ligand A, it will neither move nor rotate. I followed the exact instruction on the help section, like selecting, pressing "translate" button and moving the mouse with the ctl key. 

Can someone please shine some light on this? I am using a Mac and the software is the most recent. 

 

Thanks

 

HL

Hi,

Did you try it in MarvinSpace or MarvinSketch?

Best regards,

Akos

I tried in MarvinSpace. 

Hi Hao,

The alignment of a molecule to a natural ligand of a protein is possible in MarvinSpace. I would not call it docking because this algorithm not uses the protein surroundings but the original ligand and its conformation/pose instead.

This is how it works:

http://www.youtube.com/watch?v=AwzkCysQaog

Alignment of a molecule to a thrombin inhibitor (1DWC) with MarvinSpace.

3d
coordinates of the molecule to align is generated automatically if
there was none found. The conformation of the molecule is tweaked so as
to adapt the most to the original ligand. The protein surroundings are
not considered yet.

USAGE:
- select the original ligand
- highlight the molecule to align
- press the smiley icon on toolbar

HINT:
on
the sidebar select the "popup \ edit the the ligand with marvin sketch"
and correct the possible bond order issues in the pdb file.

 

Hope this helps. If you have further questions don`t hesitate to ask here.

Regards,

Adrian