Hi,
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.
So my question: Is there a way to consistently reorder and protonate the
structures?
For identical solvent content, I think I can approximate TIP3P conditions
by estimating the number of waters and counterions to add and using Amber's
AddToBox program.
Best,
Sunny
--
Sunny Chun
Molecular Biology Institute Graduate Student
Chemistry-Biology Interface Fellow
269 Boyer Hall, UCLA
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Received on Tue Aug 20 2013 - 15:00:02 PDT
