[gmx-users] ERROR in Membrane-protein simulation

BIJENDRA KHADKA khadkab at mcmaster.ca
Mon May 23 17:48:18 CEST 2016

Hello Everyone,
I received an error (shown below) while trying to run "Adding ion" step
Protein-membrane simulation. Any advice or suggestions will be greatly

The steps utilized proior to "Adding Ions" are mention below:

> pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water
Topology file updated (as indicated in tutorial)
> editconf -f dppc128.pdb -o dppc128.gro

> grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr

> cat KALP-15_processed.gro dppc128_whole.gro > system.gro

> editconf -f system.gro -o system_box.gro -box 6.41840 6.44350 10.59650

> solvate -cp  system_box.gro -cs spc216.gro -o system_box_sol.gro




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