On 2012-03-12 22:56, saly jackson wrote:
Hi everybody

I want to build a simulation box fill of water and some SDS molecules.
To do this at first I fill the box with SDS molecules without their Na+
ions. Then I filled the simulation box with water molecules. After that,
I want to replace some water molecules with Na+ ions. I ran the
following commands:

genbox -ci SDS.pdb -nmol 10 -box 2 2 1.9  -p topol.top -o SDS-box.gro
genbox -cp SDS-box.gro -cs spc216.gro  -p topol.top -o SDSWater.gro
grompp -f ions.mdp -c SDSWater.gro -p topol.top -o ions.tpr

But to run the last command I receive the following error:
you managed to cut the essential information before this, that would help you to fix the problem yourself.


Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

"I managed to get two hours of work done before work" (E. Lindahl)

Would you please help me,

Thanks

Saly





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