santosh naik wrote:
hi guys
i am working with the spider toxin protein and  as mentioned early i
was unable 2 over come this process

below i have mentioning my problem in detail

Thanks for that. It looks OK to me.

I've snipped out the lines where you mention the .top file
grompp -f em.mdp -c 3/out3.gro -p 1/out1.top -o 4/out4.tpr

now again i run the grompp
now here i have edited the top file
i removed 2 water molecule and added 2 cl molecules
grompp -f em.mdp -c 5/out5.gro -p 1/out1.top -o 6/out6.tpr

grompp -f pr.mdp -c 7/out7.gro -p 1/out1.top -o 8/out8.tpr

here i got he error

Fatal error:
number of coordinates in coordinate file (7/out7.gro, 7485)
             does not match topology (1/out1.top, 0)

So assuming that the contents of 1/out1.top haven't changed since you edited them, the normal reason for it failing is that it can no longer find the .itp files it needs to include. It found them earlier though, so I expect something has changed about the environment.

Mark
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