AMBER Archive (2006)

Subject: AMBER: charge redistribution in .prep files

From: Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Stefano.Pieraccini_at_unimi.it)
Date: Mon Feb 20 2006 - 06:37:54 CST

Hi all,

we built .prep files using antechamber (version 7) from gaussian output of
capped PNA fragments. In order to create the .prep files of the central
fragments we removed the capping groups from a pdb file of the residue obteined
from the .prep onece again using antechamber. Finally we created a .prep file
from the modified pdb which corresponded to the central fragment. We noticed
that the order of the atoms in this new .prep file was altered with respect to
the order in the preciding .prep file and the pdb file either. A problem arose
whem we recalculated the charges of the fragment, redistribuiting the small
excess charge on the remaing atoms, because it was not possible to make
correspoinding the new charge vector (last column of the .prep file) with the
atoms of the new file. Is it possible to obtain a .prep file with the same atom
order of the original file, or does it exist a way to know a priori what
mutations were performd in the original order (or maybe a more cleaver way to
perform our task?)

Thank you in advance

Stefano Pieraccini
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