Hi,
>> I plan to do thermodynamic integration calculations for my first time
>> using Amber. As you know, the common atoms that are present in both
[...]
>> both initial pdb files, after running tLEAP to generate the prmtop and
>> coord files, the atom ID of this proton is no longer identical. Iā€™ve
The atom numbering/naming is not crucial in TI, atoms can be renumbered if
you want. Set up your system with two softcore region masks, i.e. proton1
in the first input file, proton2 in the second. As long as all other atoms
are in the same order (which leap usually does not change) you should be
able to run TI.
>> 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
As Jason already said, changing things in the prmtop is not advised and
very difficult by hand, so unless you write and test a program to do it
for you, you are better of working on the system preparation stage (leap).
>> I guess the reason is that tLEAP renumbers the atoms based on
>> connectivities, but if I cannot circunvent this default option, I
I think leap follows the atom numbering&naming in the appropriate
residue-template, so you could change these if you really want your
softcore atoms to have the same number (which should not be necessary).
Also note: You are most likely aware of this, but MD-based TI will only
tell you something about the environment effect on the tautomerism you
study, not the 'true' deltaG, because the TI-run will include all sorts of
internal, non-physical forcefield terms. So a thermodynamic cycle has to
be set up to get a useful ddG...
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Mon Oct 31 2011 - 02:00:04 PDT
