[gmx-users] error with indexfile

Awasthi, Neha neha.awasthi at biologie.uni-goettingen.de
Fri Jan 4 09:40:44 CET 2013

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
The error is
Fatal error:
Invalid atom number 6518 in indexfile
How can i fix this ?
Thank so much for any help !
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