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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