Egidijus Kuprusevicius wrote:
*Thank you for replies. Below there are pdb file format specifications. *
*
http://www.wwpdb.org/documentation/format23/sect9.html#HETATM
*
*Are these valid for Gromacs pdb files as well? What sections are
important and should be present and what can be spared?*
Since it is a fixed-column file format, you need to have all the fields,
or fill them with spaces. It's probably the same, but I'd recommend
following http://www.wwpdb.org/documentation/format23/sect9.html#ATOM.
Either way, this will only matter if you are constructing your initial
structure for presentation to pdb2gmx or grompp or such. It would be
much more advisable to use an existing molecule builder. Off the top of
my head, columns 55 and later will usually be ignored, as would 17 and 27.
Mark
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