[gmx-users] problem with genion

[Justin A. Lemkul]

nitu sharma 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'
> 

 From genion -h: "genion replaces solvent molecules by monoatomic ions at the 
position of the first atoms with the most favorable electrostatic potential or 
at random...The group of solvent molecules should be continuous and all 
molecules should have the same number of atoms."

Insert into the solvent, not into the entire system.

-Justin

> -------------------------------------------------------
> 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
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================