[gmx-users] problem with genion

[Pawan Kumar]

Use solvent group (Group 13) for neutralization.

Pawan

On Sat, May 9, 2009 at 5:03 PM, nitu sharma <sharmanitu35 at gmail.com> wrote:

> Dear all,
>
>                    Thanks for solving lot of problem of me in doing
> membrane membrane protein simulation. Now I have a one problem I want to add
> ion to the my system by genion command
>
> for this i am following justin's tutorial  but in the genion step when i
> have put the command like this -
>  genion -s ions.tpr -o compsol-ions.gro -p topol1.top -pname NA+ -nname CL-
> -np 1
>   and I choose the 0 for adding ions to the system then I have  got the
> error like this -
>
> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
> Group     0 (      System) has 598751 elements
> Group     1 (     Protein) has  9902 elements
> Group     2 (   Protein-H) has  7778 elements
> Group     3 (     C-alpha) has  1000 elements
> Group     4 (    Backbone) has  3000 elements
> Group     5 (   MainChain) has  4000 elements
> Group     6 (MainChain+Cb) has  4922 elements
> Group     7 ( MainChain+H) has  4961 elements
> Group     8 (   SideChain) has  4941 elements
> Group     9 ( SideChain-H) has  3778 elements
> Group    10 ( Prot-Masses) has  9902 elements
> Group    11 ( Non-Protein) has 588849 elements
> Group    12 (        DMPC) has  5520 elements
> Group    13 (         SOL) has 583329 elements
> Group    14 (       Other) has 588849 elements
> Select a group: 0
> Selected 0: 'System'
>
> -------------------------------------------------------
> Program genion, VERSION 4.0.3
> Source code file: gmx_genion.c, line: 443
>
> Fatal error:
> Your solvent group size (598751) is not a multiple of 8
> -------------------------------------------------------
>
> can any suggest me what should I do to solve this problem . I am doing
> first time all these these things so if anyone can suggest me something I
> will be really thankful for him/her.
>
> Thanks a lot.
>
> Nitu Sharma
> School of life sciences
> Jawaherlal nehru university
> New delhi, india
>
>
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