[gmx-users] on pdb files structure

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jan 9 23:12:46 CET 2008

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.


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