[gmx-users] pds files without bond information

cdo cdonssim at gmail.com
Wed Feb 20 19:59:38 CET 2013

Hi all,

I'm new to Gromacs with a very basic question while I was reading tutorials.
Tried to search this but I couldn't narrow down to useful discussions so

It's simple. I saw some pdb files in the Tutorias. (such as LYSOZYME). But
this particular pdb file do not have all the connectivity information. But
still seems to work well in creating topology files. How is this possible?  

Don't I have to have all the connectivity information correctly in pdb file
to start with?  What is the minimum requirement for the pdb file to be used
in Gromacs? 

Does pdb2gmx generate bondtype and atom type information correctly even
without some connectivity information in the pdb file?    How complete
information about the structure of molecules should I have in order to
correctly generate input files for Gromacs? 

Thank you,

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