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Minor patch
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JLittlef committed Mar 19, 2024
1 parent df6f198 commit 16cc389
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Showing 2 changed files with 3 additions and 3 deletions.
2 changes: 1 addition & 1 deletion bin/mutant_maker.py
Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,7 @@ def create_mutants(pdbname: str, new_rep_cleaned, chain: str, pH: str):
mutpdb.findMissingAtoms()
mutpdb.addMissingAtoms()
mutpdb.addMissingHydrogens(pH_fl)
PDBFile.writeFile(pdb.topology, pdb.positions, open(mutant + "_fixed.pdb", 'w'))
PDBFile.writeFile(mutpdb.topology, mutpdb.positions, open(mutant + "_fixed.pdb", 'w'))


def main():
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4 changes: 2 additions & 2 deletions bin/openmm-minimise.py
Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,7 @@ def main():
pdbunfolded = str(stem + "_unfolded.pdb")
pdbfolded = str(stem + "_folded.pdb")
delta_g_list = []
for j in range(1,75):
for j in range(1,81):
simulation = setup_simulation(pdb, system)
simulation = setup_simulation(pdb, system)
init_state = simulation.context.getState(getEnergy=True, getPositions=True)
Expand Down Expand Up @@ -85,7 +85,7 @@ def main():
delta_G = init_pe - final_pe
logging.info("Minimised potential energy = %.9f kcal/mol"
% final_state.getPotentialEnergy().value_in_unit(kilocalories_per_mole))
if 3 <= delta_G:
if 1.3 <= delta_G:
delta_g_list.append(delta_G)
logging.info("Folding free energy = %.9f kcal/mol"
% delta_G)
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