[AMBER] Ligand problem in system preparation

From: Ch Bilal <ch.bilal321.outlook.com>
Date: Tue, 28 Dec 2021 09:17:56 +0000

hi Amber users,

i am working on a complex (pdb ID: 3qj4). ligand FDA has a charge -1. Whenever I try to prepare the system for simulations using antechamber, i get ligand structure with many changes in it (ligand structure output is attached). i used following commands with modifications but no use.

antechamber -i ligand1.mol2 -fi mol2 -o ligand-out.mol2 -fo mol2 -at sybyl -pf y
antechamber -i lig.pdb -fi pdb -o LIG.mol2 -fo mol2 -c bcc -nc 0.

anyone can tell what is the problem and how to fix it?

thank you.

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Received on Tue Dec 28 2021 - 01:30:02 PST
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