Dear all,
Thanks Florian and Justin for your suggestions
I am an beginner, so I am writing all the commands which I used
pdb2gmx -f *.pdb -o *.gro -p *.top
then
editconf -f *.gro -o *out.gro -c -d 0.8
genbox -cp *out.gro -cs -o *b4ion.gro -p *.top
grompp -f em.mdp -po *out.mdp -c *b4ion.gro -p *.top -o *b4ion.tpr
neutralized system
genion -s *b4ion.tpr -o *b4em.gro -pname Na -np 10 -g *ion.log
select group 12
editing in *.top file
grompp -f em.mdp -c *b4em.gro -p *.top -o *em.tpr
mdrun -s *em.tpr -o *em.trr -c *b4pr.gro -g em.log -e em.edr
grompp -f pr.mdp -c *b4pr.gro -p *.top -o *pr.tpr
mdrun -s *pr.tpr -o *pr.trr -c *b4md.gro -g pr.log -e pr.edr
grompp -f md.mdp -c *b4md.gro -p *.top -o *md.tpr
mdrun -s *md.tpr -o *md.trr -c *pmd.gro -g md.log -e md.edr
HOPE this will help to understand my problem
with regards
Anamika
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