Hi,
pdb2gmx generate the connectivity from the residue and atom sequences
(the file format specs state the order in which they appear) and the
distances between atoms. This is fairly robust as long as the
coordinates aren't unusually bad. For instance, if two carbons are
located at ~1 C-C bond length they are very likely to be bound to each
other.
Erik
On Feb 20, 2013, at 7:59 PM, cdo wrote:
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
far.
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,
Do
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