[gmx-users] pdb2gmx conversion loss of significant figures

[Justin A. Lemkul]

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.

-Justin

> Thanks in advance for your replies,
> Matt
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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