I am new to amber. My problem involves the creation of a complex using the
"combine" command in leap.
I had 1st used Autodock to dock my ligand with the macromolecule. I then
saved the least-energy ligand and calculated its RESP charge using
Gaussian. During this calculation the orientation of the ligand changes.
SO, I converted the ligand gout file to a pdb file using antechamber and
matched its conformation with the docked ligand using pyMol pair fitting.
I made the ligand prepin and frcmod files, and loaded the ligand and
receptor onto leap.
Now I have been told to use "complex = combine {ligand receptor}".
After doing minimsation,heating,equilibration, etc. I realised there was
something wrong in the complex and on checking (with "edit complex" in
leap) found that the moment I used the "combine" command, the complex does
not get docked as it is supposed to.
Is there any way to move the ligand to the correct docking position or
somehow combine them so that the position is correct? I tried using "move"
after opening it in "edit complex" but the orientation is wrong, and
"twist" makes it worse.
Thanks a lot,
Saaz.
2nd year undergraduate,
IITB
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jun 23 2012 - 06:00:02 PDT
