[gmx-users] genion error

[David van der Spoel]

Hiromichi Tsurui wrote:
> Dear Gromax users;
>
>
> I want to neutralize my system consisting of a protein and spc water
> molecules. After I determined the charge to neutralize using grompp (the
> system has -14), I entered as follows;
>
> genion -s topol.tpr -c confout.gro -np 14
> then appeared 
>
>
> Select a continuous group of solvent molecule
>
> Opening a library file /usr/local/gromacs/share/top/aminoacids.dat
>
> Group 0 ( System) has 92736 elements
>
> Group 1 ( Protein) has 4035 elements
>
> Group 2 ( Protein-H) has 3144 elements
>
> .
>
> .
>
> .
>
> .
>
> .
>
> Group 13 ( Other ) has 88701 elements
>
> Select a group:
>
>
> However, after I entered 0, error message appeared,
>
>
> Fatal error : Your solvent group size (92736) is not a multiple of 11
>
>
> When I entered 1,
>
> Fatal error : Your solvent group size (4035) is not a multiple of 11
>
>
> When I entered 2,
>
> Fatal error : The solvent group is not continuous: index[1]=1,
> index[2]=5
>
>
> When I entered 3,
>
> Fatal error : The solvent group is not continuous: index[1]=5,
> index[2]=14
>
>
> When I entered 4,
>
> Fatal error : The solvent group is not continuous: index[1]=1,
> index[2]=5
>
>
> and so on.
>
> How shold I neutralize the system ?
>   

select solvent group.

use -random option as well.
>
> Thank you for your cooperation.
>
>
>
>
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>   


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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