[gmx-users] problems with gromacs preprocessor

[Dallas B. Warren]

> 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"
> 
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
> 
> ; 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?

Not at all, as demonstrated by ...
 
> 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 !!!!!!

You removed the .itp that specifies water, spc.itp, so it is not
surprising that it no longer knows what SOL is.
 
> How can I fix these problems ?????????????????

Have a look at
http://www.gromacs.org/index.php?title=Documentation/Error down the page
in the grompp section the original error you came across is dealt with.


Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology 
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.