Hi,
You can use pdb4amber to preprocess pdb files that were generated from reduce:
pdb4maber -i ligand_h.pdb -o ligand_h_new.pdb
pdb4amber will remove all CONECT and other parts that are unnecessary for antechamber and leap.
The cause of the problem might be that no CONECT record was there for H4. If you do want a pdb file with CONECT information for future analysis, consider making the bonds in pymol and export with CONECT records for all bonds. The edited file from pymol will have atoms sorted by names and it will pass the checks in antechamber.
Bests,
Amy
From: Yang, Li-Yen via AMBER <amber.ambermd.org>
Date: Monday, September 18, 2023 at 6:28 PM
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] antechamber error: "This molecule may have more than one unit..."
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 - 16:30:02 PDT
