[gmx-users] Solvent error?

Nikolaos Michelarakis nm884 at york.ac.uk
Sat Aug 16 14:00:33 CEST 2014

These are the commands i used:

pdb2gmx -ignh -f 3ZK3-etc.pdb -o fws.gro -p fws.top

for the topology and selected my custom AMBER forcefield which i had placed
in the working directory and chose tip3 water

editconf -f fws.gro -o fws-PBC.gro -bt dodecahedron -d 1.2

for the box

gmx solvate -cp fws-PBC.gro -cs spc216.gro -o solv.gro -p fws.top

for the solvation

grompp -f em-sol-pme.mdp -c fws-b4ion.gro -p fws.top -o ion.tpr

when i try to add the ions i get the error.



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