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
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Received on Tue Jul 12 2016 - 23:30:03 PDT
