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
16231
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
missing?
Please help
Thanks
--
JORGE DAGNINO LEONE
Bioquímico
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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