[gmx-users] ligand is out side the box

RINU KHATTRI nickname.mittu at gmail.com
Fri Aug 22 11:37:57 CEST 2014

hello gromacs users
i am working on protein ligand complex with POPC membrane according to
justin (from previous mail) i built the system without ligand and
after minimization and shrink paste the ligand and edit the box size
but after solvation and water addition ligand is out side the box

grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr

genion -s ions.tpr -o system_solv_ions.gro -p topol.top -pname NA
-nname CL -nn 14

grompp -f minim.mdp -c system_solv_ions.gro -p topol.top -o em.tpr

gmx mdrun -v -deffnm em

you can see the image i have been uploaded
kindly help

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