[gmx-users] problems with gromacs preprocessor
pyaaea at leeds.ac.uk
Tue Oct 6 13:10:04 CEST 2009
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
[ 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
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
; Include generic topology for ions
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
No such moleculetype SOL
I donot know why SOL (water) didnot recognized by grompp !!!!!!
How can I fix these problems ?????????????????
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