Re: [AMBER] Unusual separation between protein and ligand

From: ABEL Stephane <>
Date: Sat, 26 Jan 2019 12:36:28 +0000


This seems caused by the PBC, you have to center your protein-ligand in the box before to compute the properties you want (for instance distance RMSD, distances, etc.) See the Amber manual for details


De : Rajarshi Roy []
Envoyé : samedi 26 janvier 2019 08:11
À : AMBER Mailing List
Objet : [AMBER] Unusual separation between protein and ligand

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*
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Received on Sat Jan 26 2019 - 05:00:02 PST
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