[gmx-users] pdb2gmx conversion loss of significant figures

Matthew Chan talcite at gmail.com
Mon Feb 7 22:25:56 CET 2011


I recently converted a PDB file to a .gro using pdb2gmx and I noticed that
the .gro truncates and rounds a digit from the atomic co-ordinates. Am I
making a mistake somewhere?

For example on atom 1, the .pdb file lists the co-ordinates:
-> 35.375  22.352 -11.970
where the .gro lists:
-> 3.538   2.235  -1.197

The command I used was 'pdb2gmx -f input.pdb -o output.gro -ff oplsaa -water
tip5p -p topol.top -i posre.itp -ignh'

I realize that the co-ordinates are converted into nm from angstroms, but
the least significant digit is lost.

Thanks in advance for your replies,
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