AMBER Archive (2004)

Subject: AMBER: savepdb vs ambpdb

From: Golebiowski Jerome (
Date: Fri Jun 11 2004 - 10:17:40 CDT

Dear amber community,
I want to perform a Gibbs simulation starting with a centered system in
my box (as required by gibbs).
Before solvation, in Xleap, I can center + alignaxes my solute and
savepdb and ambpdb both give me the same pdb.
however after solvation, ambpdb leads to a non-centered system
although savepdb in Xleap still leads to a centered one.
Has anyone encoutered such a problem ?
Can it be at the origin of the Gibbs error :
"more than 1 box length from the central box image"

Best regards


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