Re: [gmx-users] Re: rotation of a ligand

2013-05-03 Thread Justin Lemkul 



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

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] Re: rotation of a ligand

2013-05-03 Thread 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 

> 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
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