Re: [AMBER] Ligand problem in system preparation

From: David A Case <>
Date: Tue, 28 Dec 2021 09:34:43 -0500

On Tue, Dec 28, 2021, Ch Bilal wrote:
>i am working on a complex (pdb ID: 3qj4). ligand FDA has a charge
>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

You don't want this one: sybyl atom types will do you no good with Amber.
That option is there for folks who want sybyl types (which are sometimes
what is expected in a mol2 file) for other reasons.

>antechamber -i lig.pdb -fi pdb -o LIG.mol2 -fo mol2 -c bcc -nc 0.

This doesn't look right: if the ligand charge is -1, why are you setting -nc
0? Your input should give an error about having an odd number of electrons,
unless something else is amiss.

In some cases, you don't want to geometry optimized the ligand. See the
discussion in Note 7 of Section 16.2 of the Reference Manual.


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Received on Tue Dec 28 2021 - 07:00:02 PST
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