Aswathy wrote:
Dear friends,
I have pulled a ligand through the channel. Here i kept one residue at
the mouth of the channel as reference and group1 is one of the atom in
the side chain of the ligand.
Now I have the pullx file,( and here 1dz is the z coordinate of
group1-group0), but here I would like to have z-coordiante of the
ligand(instead of the single atom at the side chain)-group1. Becuase I
beleive , that will give the correct position of the ligand (please
correct me if I am wrong)
Is there any way to do this without running the SMD again?
Use g_traj on your trajectory.
-Justin
I have plotted the g_dist between the reference group and the ligand.
But that does not take the place of pullx. Please give your suggestions.
Thanks,
--
Aswathy
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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