[gmx-users] Crystallographic Ions

[Parker de Waal]

Hi Everyone,

I'm working with a protein which contains 2 crystallographic sodium ions and am experiencing trouble making the .gro file using pdb2gro using the Charmm36.ff parameters.

The two ions can be seen here:
ATOM  29009 NA    NA     1     -18.056 -14.113 -24.865  1.00  0.00          
ATOM  29010 NA    NA     2      27.831  26.294 -32.202  1.00  0.00         

Whenever I run pdb2gro the program complains that NA is not a valid atom type, however whenever I manually change the ions to atom and res type to SOD the resulting .top file does not count the molecules correctly. 
[ molecules ]
; Compound        #mols
Other               1 (should be NA+ and 2?)

If anyone could help fix this problem I would greatly appreciate it.

Best,
Parker