[gmx-users] Position restraint for ions

Marcelo Depólo marcelodepolo at gmail.com
Tue Apr 14 19:48:07 CEST 2015


I was wondering if there is any clear way to create position restraints for
ions. I am using:

*g_select -s rna_ions.gro -n index.ndx -on rna_ion.ndx -select 'group
"non-Water"'* -> to create an index for my RNA and Ions;


*genrestr -f rna_ions.gro -n rna_ion.ndx -o rna_ion.itp -fc 800 800 800* ->
to create an .itp file for them.

I am also including this new .itp file to the topology using the proper
'ifdef' statements, but I get this when I run grompp:

*Fatal error:[ file rna_ion.itp, line 1753 ]:Atom index (90849) in
position_restraints out of bounds (1-1748).This probably means that you
have inserted topology section "position_restraints"in a part belonging to
a different molecule than you intended to.In that case move the
"position_restraints" section to the right molecule.*

It seems the ions are not included as the same moleculetype as the RNA and
Gromacs see this as an error.

Would someone knows a neat way to do this?

Marcelo Depólo Polêto
Student of MSc Cell and Molecular Biology - UFRGS (Brazil)
B.Sc. Biochemistry - University of Viçosa (Brazil)

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