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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Received on Sun Oct 30 2011 - 07:00:02 PDT
