From: Alex Liu (liu.alex77_at_yahoo.com)
Date: Tue Nov 30 2010 - 09:12:36 CST
I have a pdb file for a system containing a channel ion. I neutralize the system
by adding counter ions and then I generate psf file. Then load both psf/pdb
files as in tutorial and add water box. This will generate new psf/pdb files for
the solvated system.
Now if I want to remove the channel ion, I have to generate new psf with the
same number of atoms. I removed this ion form the solvated system and just
generated the new psf file. But, after running MD, it says that:
Warning: Ignored 3645 bonds with zero force constants.
Warning: Will get H-H distance in rigid H2O from H-O-H angle.
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HT HT OT
My idea is maybe I have to remove channel ion from the original pdb file, then
generate psf again, then neutralize the system, then solvate again. if so, every
time I want to change something in pdb file I have to re-do all neutralization
and solvation again starting from the original pdb. Is that true?
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