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 <nhai.qn.gmail.com> 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 <eric.lang.bristol.ac.uk> 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 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
> >
> >
> > --
> >
> > 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.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
--
Eric Lang
BrisSynBio Postdoctoral Research Associate Modelling
Centre for Computational Chemistry
School of Chemistry - University of Bristol
Bristol BS8 1TS - United Kingdom
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Received on Wed Nov 09 2016 - 09:30:02 PST
