AMBER Archive (2009)

Subject: RE: [AMBER] parameterization of protein-ligand complex

From: cc cc (weekiang_at_live.com)
Date: Wed Sep 09 2009 - 12:41:52 CDT

>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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