[gmx-users] Re: rotation of a ligand

Justin Lemkul jalemkul at vt.edu
Fri May 3 17:43:51 CEST 2013

On 5/3/13 7:56 AM, Ahmet yıldırım wrote:
> 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

g_order calculates order parameters for lipid acyl chains and thus is not 
applicable here.

> What should I do?

Consult Chapter 8 of the manual to see if there is a program that is capable of 
calculating the quantity you are interested in.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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