[gmx-users] problems with gromacs preprocessor

Asmaa Elsheshiny pyaaea at leeds.ac.uk
Tue Oct 6 13:10:04 CEST 2009

Dear All,

 when I want to use grompp program 
 grompp -f minim.mdp -c solboxbrady.gro -p bradymod.top -o minimbrady.tpr

I got the following error message

Fatal error:
[ file "spc.itp", line 41 ]:
             Atom index (1) in settles out of bounds (1-0)

So I tried to modify the topology file by  removing the following

; Include water topology
#include "spc.itp"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000

; Include generic topology for ions
#include "ions.itp"

Since there is no needs also ions.itp , because I didnot add any ions to the structure. Is this right?

Finally, I tried to use grompp again with the modified topology file. I gety a different error message 

Fatal error:
No such moleculetype SOL 

I donot know why SOL (water) didnot recognized by grompp !!!!!!

How can I fix these problems ?????????????????


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