[gmx-users] gmx4.5.4 genion problem: No line with moleculetype 'SOL' found

[chris.neale at utoronto.ca]

For the quick fix:

1. run genion on your topology that does work. Look at this to see the  
format of the ion atom and residue names

2. Pick a few waters in the structure containing the ligand and  
replace the OW by the ion and remove the hydrogens, then fix the  
number of atoms on the second line of the file and run editconf on the  
file.

** But I wouldn't be satisfied with that if I were you. there is some  
problem here that you should uncover now before you move farther.

Show us your commands exactly (copy and paste) and perhaps we can help more.

As a side note: your topology that you presented  is going to cause  
you problems if you try to put position restraints on the water, as it  
is incorrectly ordered:

  ; Include water topology
  #include "gromos43a1.ff/spc.itp"

  ; Include ligand topoloty
  #include "drg.itp"
  #ifdef POSRES_WATER
  ; Position restraint for each water oxygen
  [ position_restraints ]
  ;  i funct       fcx        fcy        fcz
     1    1       1000       1000       1000
  #endif


-- original message --

Thank you for your suggestions.
I have checked the topology file with vim, and it looks pefectly, also, the
only problem happens when I use genion. One thing that might be possible is
that I use the double precision version of gromacs, because when I solve it
in water, the written of topology file looks weired(like I showed).
What do you mean by work-around? You mean just manually change some water
molecules in topology file and coordinate file into ions? Will the program
recognize something like CL, NA? Or can I just add ions to the system and
solve it in water?

Thank you very much

Best
Wishes