'Highlight new ligand to dock' problem

I try to use Marvin Space 5.10.0 option 'Docking a new ligand by overlaying on an existing'. I am strictly following the tutorial

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

I open PDB file of protein with a ligand. Next I open PDB file with new ligand. Old ligand is 'Selected', new ligand is 'Highlighted'. Next I click a button with smiley and I see the error:

Highlight new ligand to dock

However, my new ligand is already highlighted...

Can anybody help me?

Thanks!

I've found today that the option works if the new ligand is in 2D mrv format. If it is in PDB format (3D generated using molconvert utility) the error I mentioned above appears.

Hi Mieczyslaw,

thank you for your report. I will try to reproduce the issue You mentioned. Can you please attach the problematic protein and the ligand in pdb format here?

Thank you,

Best regards,

Adrian

Hi Adrian,

Could you send me privately your email address? I will send you the structures in attachment.

Moreover, even when I used mrv files, the final effect was not acceptable for me... the algorithm was not able to see that new ligand has the same part (ring) and it was not superimposed. We could discuss the issue to help you in improving the software.

Mieczyslaw

Hi Mieczysław,

the improper overlay is due to the errors in the representation of
the original ligand. The bond orders and atom types has issues in
the pdb file. The alignment algorithm heavily depends on them, these structure issues are the reason of the improper alignment.



I did the following steps to create the attached figure:

1. open the file protein_withATG.pdb and right click on the
   right panel on "ATG"


2. select Open in MarvinSketch


3. delete long unnecessary bonds and  LP-s, change bond types
   of the ring to make it aromatic, change the atoms eg N7 ->
   N


4. I have made these steps and saved the edited ligand. Note
   that the coordinates were not changed. See the attached
   "orig_ligand.mrv" file. To bypass the actions in step #3. ,
   you can load orig_ligand.mrv after step #1. Do not close
   components during the load.


5. load 3d_atp or new_ligand.mrv . I also changed the 3d_atp.pdb
   -> 3d_atp.mrv (see attached) prefer the mrv version.


6. hide ATG in the protein, select the edited ATG and highlight
   the ligand loaded in #5


7. press smiley icon on taskbar, or if you wish to get nicer
   alignment select Alignment\Details for pseudo dock\Systematic
   atom matching  and [Go].

Good luck.

Regards,

Adrian

Hi Mieczysław,

you asked:

 ... "is there any option to rotate the groups
around single bound" ...

Yes, there is:

1. click on the third icon on the taskbar with tooltip: "Measure dihedral of four atoms" (there is a "15" on it)


2. select four atoms of the dihedral to rotate by clickin on them. Then the dihedral monitor (green circle with arrow) appears.


3. click once on the circle. If succeeded (this was not  a trivial task for me), the circle translates a bit and its color changes from green to pale green.


4. hold( [ctrl] + [mouse click] ) + drag the mouse to rotate the dihedral.

Good luck,

Adrian