[gmx-users] error with indexfile

[Kieu Thu Nguyen]

Thank Neha ! I follow your advices but this error still appear. I don't
know why.

By the way, does anybody know why there are not ions in topology file in
Martini CG-MD. Because I see the system has not zero charge, i don't
understand why the CG system not be neutralized by ions.

Thanks and regards,
KT


On Fri, Jan 4, 2013 at 3:40 PM, Awasthi, Neha <
neha.awasthi at biologie.uni-goettingen.de> wrote:

> First check your .gro file and your .top file, to make sure atom 6518 (or
> Water) is consistently defined.
>
> Next step would be to make sure this atom features in the index file
> within a
> "correct group".
> In some cases, if a single atom is left out and not part of any group in
> the
> index file, it gives this error.
> Why not make your index file again ?
> Read the help provided with the command "make_ndx" to understand this.
> Hope that works!
>
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org on behalf of Kieu Thu Nguyen
> Sent: Fri 1/4/2013 6:51 AM
> To: Discussion list for GROMACS users
> Subject: [gmx-users] error with indexfile
>  Dear All,
>
> When using the command
> grompp -f equi.mdp -c membedded.gro -p merged.top -n index.ndx -o
> equilibrate.tpr
> The error is
> Fatal error:
> Invalid atom number 6518 in indexfile
> How can i fix this ?
> Thank so much for any help !
> Regards,
> KT
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