[gmx-users] Decomposition in minimization step

[Mark Abraham]

Hi,

mdrun can't know what your visualization preference will be, and then VMD
doesn't know how to guess either. See
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
for
tips.

Mark

On Tue, Jul 12, 2016 at 4:35 PM Yeganeh Entezari <yeganeh.entezari at gmail.com>
wrote:

> 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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