[gmx-users] Re: rotation of a ligand

[Ahmet yıldırım]

Dear users,

I tried to calculate the order parameter of benzene ring of the ligand
using g_order but I have a error as the following :
make_ndx -f topol.tpr -o order.xvg
> a C1 C2 C3 C4 C5 C6
Found 6 atoms with names C1 C2 C3 C4 C5 C6
26 C1_C2_C3_C4_C5_C6 : 6 atoms
>q
g_order -f traj.xtc -s topol.tpr -n order.ndx -order.xvg
Fatal error:
grp 1 does not have same number of elements as grp 1

What should I do?




2013/5/3 Ahmet yıldırım <ahmedo047 at gmail.com>

> Dear users,
>
> I have a ligand bound to protein. How can I calculate how much this
> ligand is rotated during the simulation time? Which tool should I use?
> g_order, g_chi, g_dih?
>
> Thanks in advance
>
> --
> Ahmet Yıldırım
>



-- 
Ahmet Yıldırım