Hello all, I am confused about what the -ignh option of pdb2gmx actually does. I have read the mailing list, the manual and many tutorials and short of browsing the source cannot find a definite answer.
The man page claims that pdb2gmx will add hydrogens, however after using the ignh option to ignore inappropriately named hydrogens in the input pdb (1xq8.pdb) there are many missing hydrogens (nearly a thousand - as far as I can tell) in the output files. Running any calculation with that many missing hydrogens seems very non-physical. It seems that pdb2gmx doesn't like the naming conventions or number of hydrogens in the pdb file. Can someone please explain what -ignh actually does and what the proper method of converting a pdb file from RCSB for use with GROMACS should be? I have tried building the protein from scratch with pymol but pdb2gmx doesn't like pymol generated pdb files either.
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