[gmx-users] Displacement of coordinates by an order of magnitude by pdb2gmx

Anna Lohning alohning at bond.edu.au
Fri Jul 7 05:36:42 CEST 2017

I've looked all through the GROMACS documentation re actions of the PDB2GMX command but I cant' see a reference to why it appears to change the coordinates of the input .pdb file (basically decreasing them by an order of magnitude). Is this normal? When grepping out your docked ligands this causes problems later when you put the ligand coordinates back in prior to creating the box, having to then alter those coordinates in the same manner. I am obviously missing some important information!  (I using Gromacs 5.0.4)
Kind regards & many thanks/Anna

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