AMBER Archive (2008)

Subject: AMBER: PDB standards

From: Francesco Pietra (
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.
francesco pietra
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)