Hello!
I tried the ligand_h.pdb with your antechamber input and it worked for
me after I removed the CONECT part of your PDB. It was also missing a
TER card at the end. Also, It looks like you have some type of lipid,
perhaps the lipid21 force field could be helpful for you?
https://ambermd.org/AmberModels_lipids.php
Hope that works!
Rodrigo.
On Mon, Sep 18, 2023 at 4:28 PM Yang, Li-Yen via AMBER
<amber.ambermd.org> wrote:
>
> 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 - 16:00:02 PDT
