Re: [AMBER] xleap numbering in residues

From: David A Case <>
Date: Thu, 20 Aug 2015 07:54:43 -0400

On Wed, Aug 19, 2015, Lara rajam wrote:
> I am trying to load a pdb file downloaded from databank.
> The residue number starts from 18 but when I load it in xleap the numbering
> is from 1 , but I would like to have the number as it is in PDB that will
> help me during analysis. how to keep the same residue numbers

The requirement inside amber to have residue numbers continuous, and starting
from 1, is deeply embedded in the code. For some sorts of analysis the
following can help:

1. use the add_pdb program to store the original residue and chain
information in the prmtop file.

2. Run your simulation.

3. use the ambpdb program (from AmberTools 15) with the "-ext" option to
convert a restart file into PDB format, with the original residue numbers.

Others on the list may want to chime in on how they handle this sort of


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Received on Thu Aug 20 2015 - 05:00:03 PDT
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