[gmx-users] Protein-ligand - genion error

Ankita naithani ankitanaithani at gmail.com
Fri Aug 10 19:05:36 CEST 2012

Dear All,

I have been trying to perform simulation for a Protein and Ligand
complex. However, when I run genion, I get an error "The solvent group
SOL is not continuous: index[37530=23341, index[3754]=23606.

I remember reading someone posting a similar problem and the solution
was provided, according to which we need to manipulate the co-ordinate
file and topology file. But, the problem is I really cannot understand
at the moment as to what exactly changes I should make in order to run
it and rectify this error.  I would be really grateful if someone
could help me and let me know as to what exactly and how I need to
incorporate the changes. Also, the co-ordinate file, should the
changes be made to the one obtained after running the genbox step?

Best Wishes,

Ankita Naithani

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