Hi Amber User,
I am trying to calculate the free energy for the protein complexes using Thermodynamics Integration. I followed the tutorial from the Amber website (
https://ambermd.org/tutorials/advanced/tutorial9/#setup_pmemd).
I have a question at step4: why we want to combine the lbnz and lphe two in the decharge combine step (which is in red text)
# coordinates for solvated ligands as created previously by MD
lsolv = loadpdb ligands_solvated.pdb
lbnz = loadpdb ligands_bnz.pdb
lphn = loadpdb ligands_phn.pdb
# coordinates for complex as created previously by MD
csolv = loadpdb complex_solvated.pdb
cbnz = loadpdb complex_bnz.pdb
cphn = loadpdb complex_phn.pdb
# decharge transformation
decharge = combine {lbnz lbnz lsolv}
setbox decharge vdw
savepdb decharge ligands_decharge.pdb
saveamberparm decharge ligands_decharge.parm7 ligands_decharge.rst7
decharge = combine {cbnz cbnz csolv}
setbox decharge vdw
savepdb decharge complex_decharge.pdb
saveamberparm decharge complex_decharge.parm7 complex_decharge.rst7
Regards
Suguna
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Received on Tue Nov 01 2022 - 20:30:06 PDT
