[gmx-users] Editconf error

Jorge Dagnino jdagnino at gmail.com
Wed May 20 23:27:50 CEST 2015

Dear GMX users.

Im trying to create my system and When i use pdb2gmx everything seems ok.

gmx pdb2gmx -f trim.pdb -o trim.gro -water spce -chainsep id

Including chain 1 in system: 3235 atoms 203 residues
Including chain 2 in system: 2531 atoms 161 residues
Including chain 3 in system: 2546 atoms 161 residues
Including chain 4 in system: 2531 atoms 161 residues
Including chain 5 in system: 2546 atoms 161 residues
Including chain 6 in system: 2842 atoms 169 residues
Now there are 16231 atoms and 1016 residues
Total mass in system 115288.734 a.m.u.
Total charge in system -17.000 e

Writing coordinate file...

--------- PLEASE NOTE ------------
You have successfully generated a topology from: trim.pdb.
The OplsaaPBS force field and the spce water model are used.

Then when i use the editconf command :

gmx editconf -f trim.gro -bt dodecahedron -o box -c -d 1.0

Read 16231 atoms
Volume: 60.3503 nm^3, corresponds to roughly 27100 electrons
No velocities found
    system size : 11.777 11.005  6.369 (nm)
    diameter    : 12.737               (nm)
    center      :   -nan   -nan   -nan (nm)
    box vectors :  4.144  4.582  3.178 (nm)
    box angles  :  90.00  90.00  90.00 (degrees)
    box volume  :  60.35               (nm^3)
    shift       :   -nan   -nan   -nan (nm)
new center      :   -nan   -nan   -nan (nm)
new box vectors : 14.737 14.737 14.737 (nm)
new box angles  :  60.00  60.00  90.00 (degrees)
new box volume  :2262.99               (nm^3)

and the ouptut file looks like this.

Giant Rising Ordinary Mutants for A Clerical Setup
   27MET      N    1    -nan    -nan    -nan
   27MET     H1    2    -nan    -nan    -nan
   27MET     H2    3    -nan    -nan    -nan
   27MET     H3    4    -nan    -nan    -nan
   27MET     CA    5    -nan    -nan    -nan

I try to make a bigger box manually, also change the box shape and the
distance but i have the same result,
This is my first time with this kind of error, what is wrong? what am i
Please help

Magíster en Bioquímica y Bioinformática
Estudiante de Doctorado en Ciencias Biológicas.
Facultad de Ciencias Biológicas
Laboratorio de Biofísica Molecular
Universidad de Concepción

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