[gmx-users] ligand in vacuum trajectories (PRODRG)

[Dariusz Plewczynski]

Dear Sirs,

I have a problem with running the short simulation with GROMACS. I have 
a structure for a small ligand (drg.pdb after cleaning with PRODRG). For 
this ligand I have run PRODRG in order to get drg.gro file and drg.itp 
topology file. I have edited the drg.top in order to include drg.itp as 
#include. My goal is to run simulation in vacuum (no water) - with only 
ligand (!). No protein also. I have tried to run it but I am getting 
error message. It seem that GROMACS does not read my topology file. What 
I am doing wrong ?

grompp -f em.mdp -c drg.gro -p drg.top -o drg.tpr


Results:
....

creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 1284 of the 1485 non-bonded parameter combinations
processing coordinates...
Fatal error: number of coordinates in coordinate file (drg.gro, 25)
             does not match topology (drg.top, 0)


Regards

Dariusz
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