[gmx-users] Re: Re: GENION: Ions inside the protein (Viswanadham Sridhara & Tsjerk Wassenaar)

Una Bjarnadottir una.bjarnadottir at ucd.ie
Wed Oct 11 18:43:17 CEST 2006

Thank you so much for your response Viswanadham Sridhara and Tsjerk 
Wassenaar Still I seem to be doing something wrong because the ions 
always end up in the active site cleft!. This is what I do: 1. I move 
the 2 watermolecules (all three atoms) which I don't want to be replaced 
at the bottom of the .gro file generated from genbox 2. Than I make 
another .gro file using genconf to renumber the atoms 3. Make a .ndx 
file from the renumbered .gro file and than delete the last 6 atoms from 
the [SOL] group 4. Run genion after grompp using the .ndx file and 
choose group [SOL] and a new .gro file is generated If you could comment 
on this than that would be highly appreaciated. Best regards, Una you 
might have deleted just one atom of water molecule. Ex: If you are using 
SPC water , you have to delete all 3 atoms in index file. Best way is to 
make changes in .gro file.. Renumber the resulting .gro file using 
genconf, make a new index file and start running. On 10/10/06, Una 
Bjarnadottir <una.bjarnadottir at ucd.ie> wrote:

>> Dear users,
>> In some of my simulations after neutralizing the systems with genion 2
>> of the ions were inside the active site cleft of the protein.
>> In the discussion on the list it was commented to either delete the
>> solvent within the protein which I did I deleted the water molecule
>> (11798) and gave genion that index file as input but than this error came:
>> Fatal error: The solvent group is not continuous: index[8198]=11797,
>> index[8199]=11799
>> I don't want to use the -random command in genion if possible because in
>> none of the other simulations I have used it.
>> Is there any other way to delete the solvent within the protein did I
>> misunderstand that so those water molecules will not be replaced?
>> Best regards, Una Bjarnadottir

More information about the gromacs.org_gmx-users mailing list