Dear Amber users!
I am performing MMPBSA based calculations of the free-energy of
binding using a trajectory sampled over 150 ns. Some additional
questions regarding protocol:
1) Dealing with the modeling of the dimeric protein where the ligand
is bound to one of the monomers, do I need to re-image my system prior
to the post-processing (avoiding jumping parts of the protein across
the PB) ?
2) What snapshot density is required for the calculations? For
example, dealing with the 150ns trajectory where each snapshot was
saved every 25000 steps, I have around 6000 snapshots. In order to
speed up the analysis, would it be OK to take each 5th snapshot for
the calculations of dH and each 10th for the dS ?
Here is my script
&general
startframe= 1, interval=${int}, keep_files=2,
strip_mask=:WAT:Cl-:Na+:K+, netcdf=1
/
&gb
igb=5, saltcon=0.150,
/
&nmode
nmstartframe=1, nminterval=5, nmode_igb=1, drms=0.05, nmode_istrng=0.15,
/
&decomp
idecomp=1,
dec_verbose=1,
/
Many thanks in advance!
Cheers
Enrico
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Received on Mon Aug 08 2022 - 08:00:03 PDT
