[AMBER] weired Ligand conformation during simulation

From: Sadaf Rani <sadafrani6.gmail.com>
Date: Sat, 30 Oct 2021 07:10:22 +0500

Dear Amber users
I am working on a protein-ligand system for which I run 100 ns of
simulation. On visual inspection I have observed that ligand adopts
unexpected conformations and as shown in pdb structures. I have used RESP
charges and antechamber for calculation of parameters.
Could you please help me to figure out the source of the problem.
Thanks in advance.
Regards
Sadaf

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ligand_conformation_at_frame_1.JPG
(image/jpeg attachment: ligand_conformation_at_frame_1.JPG)

ligand_conformation_at_frame_100.JPG
(image/jpeg attachment: ligand_conformation_at_frame_100.JPG)

Received on Fri Oct 29 2021 - 19:30:02 PDT
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