AMBER Archive (2009)

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

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On Wed, Sep 09, 2009, cc cc wrote:
>
> My objective is to conduct a production MD run on a protein-ligand
> complex and thereafter use the single trajectory obtained to calculate
> delta G using MMPBSA.
>
> 11) Run tleap:
> source leaprc.ff99SB
> source leaprc.gaff
> loadamberparams myligand.frcmod
> mylig=loadpdb mylig.pdb

Don't do this! You want something like loadAmberPrep mylig.prepi (or, load
a mol2 or off file). Loading the pdb file does *not* establish the data
structures tleap needs. (For example, there are no atom types in pdb
files...)

....dac

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