Re: [AMBER] How to fix the numbering of amino acid that got shifted in topology file that created in amber Tleap

From: Dr. Anselm Horn <>
Date: Mon, 7 Jun 2021 09:42:34 +0200

Dear Priya,

the numbering behaviour you describe is totally normal in Amber.

Amber renumbers all residues, which are read in, in a consecutive order
starting with residue number 1, and this already starts in leap during
the structure-reading step.
That may cause user confusion if explicit residue numbers are used in
leap commands (e.g. bond).

Thus, you have to keep track of the two residue numberings, one in
simulation and one system-specific. In your case, the mapping would just
be an offset of 2.
Note, that ambpdb from the AmberTools has the flag '-offset' to allow
for a shifting in residue numbering.

Best regards,


On 06/07/2021 06:11 AM, priya murugan wrote:
> Hi everyone,
> I'm currently working with protein name 5IBE which has a co-crystallised
> ligand 69M and heme cofactor in it. Since the amber force field has no
> parameter for non-standard residues and doesn't support my ligand and heme,
> I was required to generate parameters using an antechamber tool in amber by
> following the tutorial on the amber website:
> the tutorial I followed to generate a topology file for my ligand69M:
> 2.1 Simulating a pharmaceutical compound using Antechamber and the
> Generalized Amber Force Field
> <>
> following this tutorial I successfully generated parameters for my
> ligand69M and using the Shahrokh parameter in amber, I was able to generate
> topology files for the HEME cofactor in my protein.
> But now *my problem is after generating the topology file for both
> ligand69M and Heme cofactor, I realised that the numbering in my amino
> acids has been shifted for both ligand69M and Heme topology files*
> In my initial PDB file, the numbering of amino acid starts with *ALA (first
> amino acid) number 3*, but in the topology PDB file created after
> generating parameter, the amino acid number was shifted and *ALA starts
> with number 1*. So, the whole amino acids numbering sequences in the
> topology file has been shifted and not in the original right order. This
> has caused the histidine (HIS) and cysteine (CYS ) numbering to also got
> shifed in the protein topology file.
> p/s: the original PDB that I loaded in tleap had no hydrogen in the
> protein. The final topology file created had hydrogen in the protein.
> I need to use this topology file for my further work on molecular dynamic
> simulation. So, is it a normal phenomenon that can be ignored, or need
> attention and have to be fixed before start my further work? Can some
> please help me with this, please?
> Thank you in advance. Your small guide will help will bring a huge change
> to my work.
> I have attached the original PDB and topology file of my ligand69M and heme
> in the mail. I'm looking for some solution that can solve my problem.
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Received on Mon Jun 07 2021 - 01:00:02 PDT
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