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

From: William Lees <>
Date: Thu, 10 Nov 2016 10:00:46 +0000

Not actually realising that it was possible to do this in Parmed, I
wrote a small tool for my own pipleline. I thought I'd mention it as
it's a bit simpler to use and might be easier to call from a script or
to modify if it doesn't do quite what you want. It's called and is available here:


On 09/11/2016 17:16, Eric Lang wrote:
> Hi Nhai,
> No, because the original pdb doesn't have the hydrogen atoms, ions and
> water molecules, so in order to use the original pdb as the topology, they
> need to be removed from the trajectories. Because I want to keep them in
> the analysis, I cannot do that.
> Actually, I found a solution to my problem that relies on parmed and ambpdb
> and I am detailing it here if anyone has the same problem:
> First in Parmed you have to:
> - load the topology:
> parm prot.parm7
> - add the info of a pdb file that has the original residue numbering and
> chain ID:
> addPDB prot_origin.pdb
> - generate the updated topology which includes the chains and residue
> numbering information from the pdb:
> outparm prot_addPDB.parm7
> At this stage you can also generate a pdb file in parmed, it will have the
> correct residue numbering but the atom number of all atoms not present in
> the original PDB will be 99999 which it can lead to other problems so it is
> better not to do it.
> Then run ambpdb using the -ext flag:
> ambpdb -p prot_addPDB.parm7 -ext -c prot.rst7 > prot.pdb
> And the resulting PDB includes all the atoms added in tleap and also the
> original numbering and chain ID so it can be used to map
> On 9 November 2016 at 15:07, Nhai <> wrote:
>> Hi
>> Can you just use your original pdb file as topology file for analysis?
>> Hai
>>> 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
>>> 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

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Received on Thu Nov 10 2016 - 02:30:02 PST
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