AMBER Archive (2008)

Subject: AMBER: PDB standards

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Oct 13 2008 - 03:18:23 CDT

May I ask if there is any plan to update code to current PDB
standards? For example, when creating complexes with DOCK6 for
Amber10, Chimera is a quite useful intermediate vehicle. Though, atom
names like "H1" or "HD11" from Chimera are not accepted by amber, both
in Amber10 and DOCK6 amber_score, and must be transformed.As these are
not everyday procedures, one forgets how-to-do and enormous waste of
time follows, when one recognizes that neither prmtop, nor inpcrd
files for the complex are generated. I guess there may be problems of
compatibility, but present situation poses problems.
Thanks
francesco pietra
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