Hi Gabriel--
>>>
>>> Has anyone tried the water refinement protocol with protein-ligand
>>> complexes? I know the protocol uses its own parameter and topology files
>>> for proteins, but is it OK with the inclusion of extra parameter and
>>> topology files for the ligand? I modified the wrefine.py script to read
>>> in the ligand parameter file with the initParams command and
>>> pre-generated psf files with the old XPLOR structure command. The log
>>> file indicate the files are read in OK. But it complains about missing
>>> bond, angle, improper specifications for the ligand during the dynamics
>>> stage. How do I include these parameters properly for the water
>>> refinement protocol?
>>>
>> I tried and it didn’t work for me either. Same issues as you encountered.
Xu figured out what's happening:
Xu wrote:
I now realized what's happening: those parameters were in
the old protein.par but not in the water refinement protein.par.
So there's a catch: if your ligand borrows parameters from the
standard Xplor-NIH parameter file, these will likely not be
present in the parameter file used for water refinement, and will have
to be explicitly added.
best regards--
Charles
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