[gmx-users] pdb2gmx -ignh

Alexander Alexander alexanderwien2k at gmail.com
Wed May 4 11:03:36 CEST 2016

Dear GMX user,

As you know, naming the Hydrogen atom differently in different FF and in
.pdb or .gro file brings lots of problems in the "gmx pdb2gmx". I also met
the issue when I wanted to convert my self-made (by Avogadro)
heptapeptide.pdb to heptapeptide.gro file.

I could get rid of them using "-ignh" which is ignoring H atom in the
heptapeptide.pdb file.Then, If I understood correctly this means no normal
Hydrogen atom there is in produced heptapeptide.gro file?! If so, do you
think if this makes sense proceed further with a peptide which is missing
the normal hydrogen atom in?


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