[AMBER] Unusual separation between protein and ligand

From: Rajarshi Roy <phd1701171011.iiti.ac.in>
Date: Sat, 26 Jan 2019 12:41:34 +0530

Dear AMBER users and developers,
I am performing a md simulation of a pentamer protein with ligands. Each
monomer is having a ligand. But in case of two monomer among five, ligands
are separated up to 50 angstroms and again came back to its original
binding position. However, this kind of separation is not showing if I run
a movie of all this trajectory files or creating pdb of all this frames
using ambpdb command. Only, if I use trajin and trajout command to extract
that frame it is showing. I think there must be some error in simulation or
visualization or something else. Another unusual thing is found from the
pdb that the same ligand is showing in completely opposite site of the
protein. I am not able to make any sense from this trajectory . I also
attached the plot of the distance between ligand and the protein. Red one
is showing the unusual separation where the other ligand (green) stays in
the neighborhood of the protein.
Please suggest what will be possible explanation regarding this.
Thank you in advance.
-- 
*with regards*
*Rajarshi Roy*
*PhD Research Scholar*
*Biosciences and Biomedical Engineering*
*Indian Institute of Technology, Indore*
*India*



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Received on Fri Jan 25 2019 - 23:30:02 PST
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