[gmx-users] problem while running grompp Pocition restrined dynamics

Mark Abraham Mark.Abraham at anu.edu.au
Wed Apr 12 09:58:42 CEST 2006

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.


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