[gmx-users] pdb2gmx conversion loss of significant figures

Justin A. Lemkul jalemkul at vt.edu
Mon Feb 7 22:53:34 CET 2011

Matthew Chan wrote:
> Hi,
> 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.

Both .gro and .pdb files have a fixed format, so the number of digits is 
hard-coded.  I've never had a problem with accuracy while using 
single-precision.  Strictly speaking, you don't need to use .gro format for 
anything in Gromacs; you can keep .pdb if you prefer.


> Thanks in advance for your replies,
> Matt


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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