[gmx-users] pds files without bond information

Erik Marklund erikm at xray.bmc.uu.se
Wed Feb 20 21:58:07 CET 2013


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  


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  
> 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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