[AMBER] antechamber error: "This molecule may have more than one unit..."

From: Yang, Li-Yen via AMBER <amber.ambermd.org>
Date: Mon, 18 Sep 2023 22:27:48 +0000

Hello,

I am currently using antechamber to parameterize my ligand with this command:
“antechamber -i ligand_h.pdb -fi pdb -o ligand.mol2 -fo mol2 -c bcc -s 2 -nc 0”

It worked fine on the same ligand before, but somehow, I am now getting this error:

“This molecule may have more than one unit.
       antechamber can only handle one unit. If the input is a single unit
       then the connectivity is wrong and the geometry may be bad.
       Please convert your molecule to a mol2 file via:
       antechamber -j 5 -at sybyl -dr no
       And then check your molecule with a visualization program;
       manually add missing bonds or delete unwanted bonds as appropriate.”

I have attached the pdb file of the ligand.
Can anyone please give some guidance on how to solve this problem?

Thank you!
Best,
Zoey


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Received on Mon Sep 18 2023 - 16:00:01 PDT
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