Re: [AMBER] preparing parameter files for a ligand

From: Siavoush Dastmalchi <>
Date: Wed, 16 Sep 2020 17:37:22 +0430

Dear Dave,

Thanks a lot. Antechamber solved the problem.



From: David A Case (
Date: 1399-06-26 17:00
To: AMBER Mailing List (
Subject: Re: [AMBER] preparing parameter files for a ligand

On Tue, Sep 15, 2020, Siavoush Dastmalchi wrote:
>Dear List,
> I have extracted the coordinate lines
>corresponding to the ligand into a file and then applied "reduce"

It looks like your your "lig.pdb" file already has hydrogens, so there
is not need for reduce. [Aside: reduce uses a HETATM database to look
for hydrogens, so it won't necessarily know what to do with a residue
called "LIG".]

However, your structure has a couple of problems. First, the atom names
are not unique (all carbons are called "C", etc.).
You also have a very bad contact between two hydrogens, that may cause problems.

>> lig = loadpdb lig.pdb
>Loading PDB file: ./lig.pdb
>-- residue 584: duplicate [ C] atoms (total 26)
>-- residue 584: duplicate [ H] atoms (total 23)
>-- residue 584: duplicate [ O] atoms (total 6)

This is the bad naming problem, and will need to be fixed. One way to
do this is to use antechamber to convert your lig.mol2 file back to pdb
format. If you examine that file, you should see that the atom names
are now all unique. OR, you could revisit how you "extracted the
coordinate lines" for the ligand -- were the names unique at that point?
[It's possible that your reduce runs gave you problems.]


AMBER mailing list

AMBER mailing list
Received on Wed Sep 16 2020 - 06:30:04 PDT
Custom Search