Hello,
If you look inside the prmtop file, there is a section that starts with
%FLAG RESIDUE_LABEL
that stores the sequence of residues. You should be able to tell there if
the 24th and 25th residues are K+. I would imagine that the ordering in the
PDB file would be preserved, but you can also use a visualization program to
check and make sure (i.e. VMD). Whatever the prmtop has in the beginning of
the simulation, however, is conserved throughout the entire simulation (if
you wanted to, for instance, look at diffusion of those specific K+ ions).
All the best,
Jason
On Tue, May 25, 2010 at 2:31 AM, Asfa Ali <asfa.iisc.gmail.com> wrote:
> Hi,
>
> Actually the crystal structure of the pdb originally had three K+ ions. I
> have removed the K+ ion at residue 23 and saved the pdb file for my use, as
> a result my initial pdb file(1kf1_w.pdb) has K+ ions at residue no.24 and
> 25.
>
> Now after the final production run, I want to see whether the initial K+
> ions are intact or they have migrated to some other place. So I want to
> distinguish the two initial K+ ions from the solution K+ ions provided by
> AMBER.
>
> So will the initial K+ ions still be numbered 24 & 25 after the final prod
> run?
>
> The two pdb files are attached earlier.
>
> Thanks,
> Asfa.
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue May 25 2010 - 05:30:04 PDT
