[gmx-users] Unable to neutralize my system

[namita at ncbs.res.in]

Thanks for the suggestions but just to make my problem more clear....

The "genion" command that I used is:

/opt/gromacs/bin/genion_mpi -s em.tpr -o ce_myoII_frag0_neu.gro -g
genion.log -np 2 -pname Na+

And the topology file is:

Before adding ions:

[ molecules ]
; Compound        #mols
Protein             1
SOL           2818598

After adding ions: (modified)

[ molecules ]
; Compound        #mols
Protein             1
SOL           2818600
NA+                 2




Dear All

When I run the command "genion" specifying the number n type of chrges to
be added, it works fine. I also have made changes in my topology file. But
somwhow when I run the "grompp" after that it gives me the following
error...

processing topology...
Generated 380 of the 1326 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
Excluding 2 bonded neighbours for SOL 2818600
Excluding 1 bonded neighbours for Na+ 2
NOTE:
  System has non-zero total charge: -2.399999e+01

processing coordinates...
-------------------------------------------------------
Program grompp_mpi, VERSION 3.3.1
Source code file: grompp.c, line: 448

Fatal error:
number of coordinates in coordinate file (ce_myoII_frag0_neu.gro, 8461523)
             does not match topology (ce_myoII_frag0.top, 8461535)
-------------------------------------------------------

I tried adding 2 and 3 ions to the system. But it seems to give the same
error. Could someone help?

Thanks
Namitha Mohandas