AMBER Archive (2004)

Subject: AMBER: Problem with a single aminoacid as inhibitor

From: Daniel Wetzler (
Date: Wed Nov 17 2004 - 05:59:12 CST

Dear Amber-users,

I have a problem with a single aminoacid which acts like a inhibitor for
a enzyme I'm dealing with.
My problem is, that this aminoacid should be fully protonated (NH3-group).
Regardless how I write this structure into my pdb-files (in its own
chain, as HETATM
a.s.o) xleap seems to handle it like a part of my structure and
protonates my N only with one H.

If I protonate my structure with the protonate command I get the right
structure with NH3
but after using xleap to write the .top / .crd files I get the
deprotonated form again.

Does anyone know how to change that behaviour ?

Hope anyone can help.

Best wishes,

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