[gmx-users] editconf- pdb to gro format

[Juliette N.]

Hi all,

I am trying to produce gro file from PDB file using editconf.

Here is the pdb file

HETATM    1  C                   0.672  -0.000
0.000                       C
HETATM    2  C                  -0.672  -0.000
0.000                       C
HETATM    3  H                   1.238  -0.928
0.000                       H
HETATM    4  H                   1.238   0.928
0.000                       H
HETATM    5  H                  -1.238  -0.928
0.000                       H
HETATM    6  H                  -1.238   0.928
0.000                       H

Then I use: editconf -f X.pdb -o X.gro

But the go file seems no to be correct

    6
    0         C    1   0.067  -0.000   0.000
    0         C    2  -0.067  -0.000   0.000
    0         H    3   0.124  -0.093   0.000
    0         H    4   0.124   0.093   0.000
    0         H    5  -0.124  -0.093   0.000
    0         H    6  -0.124   0.093   0.000
   0.00000   0.00000   0.00000

Can anyone please help why this is happening?

Thank you!

-- 
Thanks,
J. N.