[gmx-users] Problem with grompp , ffamber99 and ions

[Gunnar Widtfeldt Reginsson]

Hi.I am trying to run this command on a solvated DNA

grompp -f mini_sol.mdp -p topol.top -c DNAneutral.pdb -n DNAneutral.ndx

and I get this fatal error:
-------------------------------------------------------
Program grompp, VERSION 4.0.5
Source code file: toppush.c, line: 1641

Fatal error:
No such moleculetype Na+
-------------------------------------------------------

I have added to the file ions.itp :
[ moleculetype ]
; molname       nrexcl
Na+             1

[ atoms ]
; id    at type res nr  residu name     at name  cg nr  charge
1    amber99_31 1       Na+             Na       1      1


because this is how the Na ion is in ffamber99.rtp


[ Na+ ]
 [ atoms ]
   Na     amber99_31   1.00000     1

And this I have done according to the amber website:
http://chemistry.csulb.edu/ffamber/#aadat


The last part of the topol.top file is:
SOL         13651
Na+         38
Cl          0

and the structure file contains:
ATOM  55905  Na  Na+  3729      77.070  47.215  21.822  1.00  0.00

Does anyone know what could be wrong?

Thanks.
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