On Thu, Mar 17, 2011, Andre Serobian wrote:
> The H2'1 and H2'2 names were created in the pdb file when I used
> ambpdb -aatm to make the pdb file.
Ah: you are correct. Although it is not stated as such, the -aatm option
should now rarely be used, and you should try leaving it out. (The problem you
are seeing is that the "94" version of the Amber libraries used names more
like those in PDB version 2, whereas the map.DG-AMBER file has been upgraded
to version 3. With the upcoming release, everything in Amber should be more in
sync with PDB version 3.)
....dac
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Received on Thu Mar 17 2011 - 06:00:02 PDT
