>normally one would dock molecules, then
> solvate and equilibrate.
The difficulty I am experiencing is the parameterization of the protein-ligand complex. As mentioned, I have successfully obtained the parameters for the ligand (without the protein) but I do not have any success when I conduct the tleap procedure using the complex structure. I was trying to emulate the steps described in
http://www.rosswalker.co.uk/tutorials/psc_workshop/Tutorial_six/using_leap_complex.html
I am interested to know how to parameterize a protein-ligand complex. In the "Fatal" error messages, all the atoms involved are the ones belonging to the ligand which was concatenated with the protein.pdb file.
thank you.
Jeff Yeo
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Received on Mon Sep 14 2009 - 13:38:25 PDT
