[gmx-users] Decomposition in minimization step

[Yeganeh Entezari]

Hi,
I have a problem after this step:

grompp -f em.mdp -c sol_ions.gro -p topol.top -o em.tpr
mdrun -v -deffnm  em

 I achieved the ligand parameters from ANTECHAMBER that are usable for
GROMACS software.
After using this command line :

 $AMBERHOME/exe/ambpdb -p lig.prmtop < lig.inpcrd > lig.pdb

The pdb structure of ligand visualized with VMD and it was OK, but after
minimization step when I see em.gro and em.trr file in VMD I saw that the
structure of ligand in a protein is broken and a series of unusual bonds
are fromed.


Apparently all parameters are correct and I don't have any Warning or Notes
in each steps but I don't know where the problem is in this stage.

I'm really appreciate if you could help me,

Regards,

Yeganeh