[gmx-users] ignoring -h atoms

maria khan mariabiochemist1 at gmail.com
Wed Feb 8 07:20:31 CET 2017

Dear ERIK..

"""..No. -ignh ignores the hydrogen atoms in the input structure, but uses
the rtp file(s) to generate new hydrogens. This is useful, for example,
when some hydrogens are missing in the pdb file. The structure and topology
will therefore contain hydrogens in the end also with -ignh."""..

now i have confusion if the ff ist ignore it and then in rtp files consider
it..so why it at ist it ignores..there is no need to do so.after all h-atom
will be same if it is in input file or when later form by rtp file.

secondly what will be the consequences,,if in case it is ignored or not
ignored..would it make difference to results in both cases.and if there
would difference in results,,what kind of results are more reliable.???


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