Dear amber developer,
I have used MMPBSA.PY to calculate entropy, but there are some process I don't understand. The mmpbsa.in file as following:
&general
verbose=1, keep_files=2, use_sander=1,
startfram=2001, endframe=2006, interval=5,
/
...
/
&nmode
nmstartframe=1,
nmendframe=2,
nminterval=1,
dielc=1.0,
drms=0.001,
maxcyc=10000,
nmode_igb=1,
nmode_istrng=0.0,
/
The process file pbsa.log as following:
....
2 frames were processed by cpptraj for use in calculation.
2 frames were processed by cpptraj for nmode calculations.
Running calculations on normal system...
Beginning PB calculations with /home/haomiao/md/amber16/bin/sander
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning nmode calculations with /home/haomiao/md/amber16/bin/mmpbsa_py_nabnmode
calculating complex contribution...
Line minimizer aborted: step at upper bound 0.070443205
Line minimizer aborted: step at upper bound 0.00067657615
Line minimizer aborted: step at upper bound 0.0004082432
Line minimizer aborted: step at upper bound 0.011483969
Line minimizer aborted: step at upper bound 0.011409417
Line minimizer aborted: step at upper bound 0.046362475
Line minimizer aborted: step at upper bound 0.0001097595
calculating receptor contribution...
Line minimizer aborted: step at upper bound 0.0023964902
Line minimizer aborted: step at upper bound 0.050352631
Line minimizer aborted: step at upper bound 0.0015487836
calculating ligand contribution...
Line minimizer aborted: step at upper bound 0.086856859
Line minimizer aborted: step at upper bound 9.4704377e-05
Line minimizer aborted: step at upper bound 0.0017161722
Line minimizer aborted: step at upper bound 0.0054606726
Timing:
Total setup time: 0.002 min.
Creating trajectories with cpptraj: 0.015 min.
Total calculation time: 5.222 min.
....
I want to know the mean about "Line minimizer aborted: step at upper bound 0.0054606726" ,and how to deal with it?
and the outputfiel final-result-mmpbsa.dat as following:
......
MMPBSA.py Version=14.0
|Solvated complex topology file: charge_prmtop
|Complex topology file: pbsa_com_prmtop
|Receptor topology file: pbsa_rec_prmtop
|Ligand topology file: pbsa_lig_prmtop
|Initial mdcrd(s): 03_Prod_1.mdcrd.1
|
|Receptor mask: ":1-51"
|Ligand mask: ":52-102"
|
|Calculations performed using 2.0 complex frames.
|NMODE calculations performed using 2.0 frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in sander.
|
|All units are reported in kcal/mole.
|All entropy results have units kcal/mol (Temperature is 298.15 K).
....
In my simulation, the temperture is 300K, why the calculation temperature is 298.15K? And how to compute entropy under 300K?
Thanks.
Qiankun
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Received on Thu Sep 13 2018 - 00:30:02 PDT
