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

From: Nhai <>
Date: Wed, 9 Nov 2016 10:07:40 -0500


Can you just use your original pdb file as topology file for analysis?


> On Nov 9, 2016, at 6:44 AM, Eric Lang <> wrote:
> Hello,
> 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 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
> --
> 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

AMBER mailing list
Received on Wed Nov 09 2016 - 07:30:02 PST
Custom Search