[AMBER] Mapping back the original PDB numbering and chain IDs when analysing Amber trajectories

From: Eric Lang <eric.lang.bristol.ac.uk>
Date: Wed, 9 Nov 2016 11:44:02 +0000


I am working with a heptameric protein and during the preparation of the
system in Amber, all the residues are renumbered in a sequential order and
the chain IDs are removed.

When I analyse my trajectories in VMD or with another program, I am
therefore not able to use the original residue numbering scheme, which is
not really practical. For example, if I am interested in residue number 23
in chains E and G (original numbering scheme) I have to calculate the
corresponding Amber residue numbers in order to select the correct residues.

If I use pdb4amber.py to prepare the original pdb file, a _renum.txt
outpout file is generated that connect the new residue numbering scheme to
the original one.Is there a way, when I process my trajectories in CPPTRAJ
for example to use this _renum.txt or the original PDB to map back the
original residue numbering scheme and the chain IDs to the trajectories so
the processed trajectories use this original numbering and therefore it is
much more convenient to analyse the trajectories in VMD of another program?

Alternatively, is there a way in tleap or Parmed to generate a file that
has the original residue numbering and the topology information (a bit like
the original PSF file when running simulation in Amber using the charmm
force field)?

I haven't seen anything like that in the manual or mailing list but I might
have missed it.

Has anyone any alternative method they use to deal with this when working
with multimeric proteins?

Many thanks in advance,


Eric Lang
BrisSynBio Postdoctoral Research Associate Modelling
Centre for Computational Chemistry
School of Chemistry - University of Bristol
Bristol BS8 1TS - United Kingdom
AMBER mailing list
Received on Wed Nov 09 2016 - 04:00:02 PST
Custom Search