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Consistency of interface DDG calculations

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Consistency of interface DDG calculations

Hello, I have been trying to validate interface energies computed using Rosetta 2.3, but have been having some difficulty obtaining agreement between two expressions that should be equivalent.

I start with a protein with two chains in a single PDB file, ab.pdb.

Then I run Rosetta++ with the following flags:
-interface -ddg_bind_only -s ab.pdb -intout ab.txt -output_structure -Wpack_only -relax_unbound false

This gives me three files:
ab_nat_0001.pdb (A chain only)
ab_nat_0002.pdb (B chain only)
ab_nat_0003.pdb (A+B chains together)

along with the following energies:
dG = E(AB) - E(A) - E(B) = (1253.7) - (672.7) - (639.4) = -58.4 final dG

Then I take each of the ab_nat_000*.pdb files, and rescore them using the following flags:
-s ab_nat_0001.pdb -score -fa_input -intout score.txt -overwrite -scorefile a.score

This time I obtain
E(AB) - E(A) - E(B) = (1253.7) - (669.5) - (634.4) = -50.3

which is different by 8 kcal/mol, because the energies of A and B are now different when scored separately.

The inconsistency persists despite trying many changes:
-- using softened potentials
-- relaxing structure beforehand
-- setting relax_unbound to false

Does anyone have any idea what could be causing these energy differences? Thanks!

ab.pdb_.txt232.96 KB
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Sun, 2014-03-30 21:35