On Tue, Aug 20, 2013, Sunny Chun wrote:
>
> I would like to use Targeted MD to get coordinate snapshots of my structure
> going from "closed" to "open" conformations, and vice versa. I have each
> "closed" and "open" structures of the same sequence but the pdb files have
> different atom order (per residue) and residue numbering scheme (e.g.,
> numbering starting from #2 instead of #1 and chain names). They also are
> treated differently upon solvation (more solvent added to one structure
> than the other). Furthermore, using protonation servers (e.g., PDB2PQR)
> produces different protonation states for each structure. That would all be
> fine, except that Targeted MD requires the reference and input coordinates
> to match the same topology file.
The order of atoms inside residues is irrelevant (Amber will reorder them
upon input). Ditto for the residue and chain numbers: Amber renumbers
residues starting at 1 and continuing on -- so as long as the total residue
count and and order is the same you should be fine.
You will need to have a consistent protonation scheme: choose one or the other
or some compromise.
...good luck...dac
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Received on Tue Aug 20 2013 - 19:00:02 PDT
