[gmx-users] problem with genion

nitu sharma sharmanitu35 at gmail.com
Sat May 9 13:33:13 CEST 2009

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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