Chih-Ying Lin wrote:
Hi
I have a protein+several ligand in the simulation box.
After 5ns, the protein drift to the right edge of the box and the
ligand drift to the left edge of the box.
I am very sure that the ligand has attached to the protein.
with this command =
trjconv -pbc nojump -center rect
This is not a correct command; -center does not take an argument. In any case,
I have found that trjconv -pbc mol -ur compact -center (and choosing 'Protein'
to be centered) works quite well.
-Justin
so, how can i use trjconv command to see protein-ligand complex as a whole?
Thank you
Lin
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--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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