[AMBER] tleap strange behavior

From: Ignacio J. General <ijgeneral.gmail.com>
Date: Wed, 23 Mar 2011 11:45:29 -0400

Dear Amber users,

I just want to report a strange behavior I found in tleap, when trying to
manipulate some parameter files for use with Thermodynamic Integration.

I have two input scripts for tleap, both read the gaff parameters of a
ligand, then load a pdb of ligand + water, and remove the ligand. Finally,
they both write the new parameters and coordinates. Both should do exactly
the same thing but for some reason I can't figure out they don't. The
difference in the resulting parameter files is, apparently, minor, just two
numbers swapped in %FLAG BOND_EQUIL_VALUE and the order of many numbers
inverted in %FLAG BONDS_INC_HYDROGEN. In principle, although strange, I
guess it shouldn't be a problem, probably tleap just reversed the order of
some atoms. But when I try to do TI using these files, it doesn't work, it
just stops without any warning or error.

The reason it doesn't work in TI could be just that TI needs the two
parameter files (processes v0 and v1) to be (almost) exactly the same, so it
wants the order of atoms to be equal. But since the whole things sounds to
me suspicious, I just wanted to let the people involved in the development
of tleap of this, it may be pointing to some bug...

If anybody wants to look deeper into this, here I attach the files I'm



PS: Note that the attached file SB.doc is really SB3.lib (gmail didn't like

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Received on Wed Mar 23 2011 - 09:00:03 PDT
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