Hi all,
I am running MMPBSA calculations (parallel version) in the latest
AmberTools. I am trying to write "DELTA TOTAL" and Total energy
decomposition (DELTAS) in the same calculation. See the input file below :
&general
startframe=1, endframe=2500, interval=20,
strip_mask=:WAT:CL:CIO:CS:IB:K:LI:MG:NA:RB:Na+:Cl-,
verbose=2, keep_files=0,
receptor_mask=:1-234, ligand_mask=:235-237,
/
&pb
indi=1, exdi=80, radiopt=0,
fillratio=4.0, istrng=0.15,
linit=1000, prbrad=1.4, scale=2.0,
cavity_surften=0.0378, cavity_offset=-0.5692,
/
&decomp
idecomp=1, print_res="1-237"
dec_verbose=1, csv_format=0
/
I see a discrepancy in the "DELTA TOTAL" (+4.9 Kcal/mol) and sum of numbers
in "Total" column for all the residues in per residue decomposition data.
The sum of "Total" column for all the residues (including protein,ligand
and two ions) is -9.2. I expect this sum to be +4.9 of close to it. Is
there something I am missing ? What want to calculate is the contribution
of each residue in overall free energy (+4.9). You can see both the files
(-o FINAL-PBSA-GB1.dat and -do DECOMP-PBSA-GB1.dat) for this calculation.
Sincerely,
Mish
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Received on Wed Apr 12 2017 - 02:00:02 PDT
