> If you simple replace HETATM with ATOM, i.e.:
>
> :1,$s/HETATM/ATOM/
>
> you shift all columns left by two characters. This is probably why, instead
> of
> reading GLY, pdb2gmx is reading Y only. The proper replacement would be:
>
> :1,$s/HETATM/ATOM /
>
> Note the two trailing spaces after ATOM.
>
> -Justin
Justin, adding the two spaces did the job. Thanks
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