[Xplor-nih] Water refinement for protein-ligand complexes

[Xu Wang]

Hi

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?

Xu Wang
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[Charles Schwieters]

Hello Xu--

Post by Xu Wang
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 don't believe anything special is required, but something needs to
be fixed. Could you please send the script and log file? [You can send
these to me privately, if you wish.]

best regards--
Charles

[Gabriel Cornilescu]

I tried and it didn?t work for me either. Same issues as you encountered.

Post by Xu Wang
Hi
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?
Xu Wang
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[Charles Schwieters]

Hi Gabriel--

Post by Gabriel Cornilescu

Post by Xu Wang
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