On Sat, May 26, 2012, Francesco Pietra wrote:
> Coming to AMBER ff12SB with a protein extensively equilibrated with
> CHARMM 27 ff, I wonder whether it is worth trying to save the initial
> position of H-atoms.
Attached is the script I use for CHARMM-pdb files for proteins. It won't work
for non-protein things, so you would have to either apply it to the
protein-only part, then reassemble things, or make the script smarter.
It's probably best not to discard the hydrogens and rebuild them: for some
protons, it won't make a difference, but will be important for things like
Thr/Ser/Tyr to get good initial hydrogen bonding.
You could also ask on the CHARMM forums for advice on how to create PDB files
that correspond to the PDB standard: this problem must come up a lot.
....dac
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Received on Sun May 27 2012 - 06:30:02 PDT
