Changing the order of atoms in a topology file is very difficult, and
impossible by hand (in practice). You should view the tautomeric hydrogens
as different atoms. As I recall, the softcore code can deal with atoms
that exist in one system, but not in the other. You just have to make sure
that the remaining atoms are in the same order. An alternative is to use
dummy atoms, and have those disappear just by eliminating the charges where
they technically don't exist in that system.
HTH,
Jason
On Sun, Oct 30, 2011 at 9:47 AM, Gonzalo Jimenez <gjimenez.chem.ucla.edu>wrote:
> Dear all,
>
> I plan to do thermodynamic integration calculations for my first time
> using Amber. As you know, the common atoms that are present in both states
> need to appear in the same order in both prmtop files and must have
> identical starting positions. My problem is that I want to analyze a
> tautomerism equilibrium and, thus, the atom that is changing from one state
> to the other is a proton. Although I start from identical atom numbering in
> both initial pdb files, after running tLEAP to generate the prmtop and
> coord files, the atom ID of this proton is no longer identical. I’ve tried
> to change it by hand on the prmtop files, but while the position of the
> atom is easy to change, the charge and other flags is much more complicated.
> I guess the reason is that tLEAP renumbers the atoms based on
> connectivities, but if I cannot circunvent this default option, I basically
> cannot run TI, right?
>
> Any piece of advice on this, please?
>
> Thanks a lot,
>
> Gonzalo
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Oct 30 2011 - 14:30:06 PDT
