Dear AMBER users,
I want to calculate the free energy associated to Na+ binding using TI. I
would like to transform it into a water molecule while at the same time
transforming a water molecule in the bulk by another Na+ to keep the
neutrality. I try to create two topology files for both ending states (I
have only AMBER12) but Leap keeps on changing the residue order. There is
no problem when creating the initial state (Na+ in the binding site and WAT
in the bulk, Na+ appears before WAT in the input pdb file) but if I edit
the pdb to create the final state (WAT in the binding site and Na+ in the
bulk, this time WAT residue appears before Na+) then Leap changes the
residue order. It seems like it puts all Na+ ions first and then the water
molecules without taking into account the input order from the pdb file.
Briefly:
Input PDB- Initial state (Na+ in the binding site and WAT in the bulk)
ATOM 19848 Na+ Na+ 1296 -6.729 -14.447 0.924 1.00 0.00
TER
ATOM 19849 O WAT 1297 -9.981 22.147 -1.135 1.00 0.00
ATOM 19850 H1 WAT 1297 -9.023 22.147 -1.135 1.00 0.00
ATOM 19851 H2 WAT 1297 -10.220 23.073 -1.135 1.00 0.00
TER
Input PDB - Final state (WAT in the binding site and Na+ in the bulk)
ATOM 19848 O WAT 1296 -9.981 22.147 -1.135 1.00 0.00
ATOM 19849 H1 WAT 1296 -9.023 22.147 -1.135 1.00 0.00
ATOM 19850 H2 WAT 1296 -10.220 23.073 -1.135 1.00 0.00
TER
ATOM 19851 Na+ Na+ 1297 -6.729 -14.447 0.924 1.00 0.00
TER
When using Leap with the latter, it creates a system in which WAT and Na+
are order-reversed avoiding to use the topology file for TI calculation.
If this helps, I have tried to create a new library for the WAT molecule
(new residue name but the same WAT info) with no luck.
Could you suggest me a way to keep the order of the residues from the input
PDB? Or an alternative?
Thanks.
Ignacio
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Received on Wed Jul 01 2015 - 09:30:03 PDT
