[gmx-users] inconsistency in .pdb files

[Mark Abraham]

h a wrote:
> Dear users,
> 
> I am a beginner with gromacs. I converted a sample pdb file to gromacs 
> file using "pdb2gmx" and then converted it back to pdb file using 
> "genconf" but I found that positions of atoms was changed and so was 
> their thermal factor. I did not understand why there was change in 
> position of the atoms. 

 From genconf -h "genconf  multiplies  a given coordinate file by simply 
stacking them on top of each other, like a small child playing with 
wooden blocks." Thus you should be expecting position changes!

The .gro format doesn't have thermal factors, so neither will any format 
  using a structure derived from such a file.

Also, there's no GROMACS-related need for you to want to regenerate a 
PDB file... any structure file format will do... See 
http://wiki.gromacs.org/index.php/Coordinate_File#On_the_need_for_a_.gro_file

> when I observed both of them using pymol I found  
> inconsistency in type of atoms and bond locations.
> 
> can you please explain why this happened .

No, because "inconsistency" is too vague to be understood. We need to 
know what you did, what you saw, what you expected and why you thought 
something was wrong.

Mark