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

[santosh naik]

no i have given the right path only
even i have checked the top file 2
do that first md run can make any harmful changes in top file


On 4/12/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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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