Update: I was able to figure out how to use the program thanks to this 2013 thread: http://archive.ambermd.org/201302/0412.html
At the same time, I think I made a weird discovery-regarding the input coordinates (the last flag) for mmpbsa_py_nabnmode, the results are different if it is a NetCDF file or ASCII file! I was comparing the MMPBSA.py results with the direct mmpbsa_py_nabnmode results, debugging bit by bit, and ultimately found out. MMPBSA.py generates the .nc format. When I initially used the ASCII format for coordinates input, the beginning of the output from nabnmode has huge energies. This does not happen with the .nc file. The structures are exactly the same. Here are the copy and pasted results:
Processing NETCDF traj
iter Total bad vdW elect nonpolar genBorn frms
ff: 0 26.39 44.14 -5.48 128.73 0.00 -141.01 1.99e+00
Starting TNCG minimisation
MIN: Iter = 0 NFunc = 1 E = 26.39067 RMSG = 1.9867697e+00
CG: It= 4 ( 0.493)q :-)
LS: i= 1 lhs_f= -0.5415752 rhs_f= -0.00010735662
lhs_g= 0.01470948 rhs_g= 0.96620955
rel_s= 1 abs_s= 0.066076962
max_d= 0.031979483 i_xyz= 66x
LS: step= 1 it= 1
MIN: Iter = 1 NFunc = 6 E = 25.84897 RMSG = 6.2138831e-01
CG: It= 50 ( 0.879)q :-(
LS: i= 1 lhs_f= -0.76271756 rhs_f= -8.3663814e-05
lhs_g= 5.9459457 rhs_g= 7.0676583
rel_s= 0.10653802 abs_s= 0.48739729
max_d= 0.15 i_xyz= 64y
LS: step= 0.10653802 it= 1
------------------------------------------------------------------For the ASCII input version:
Processing ASCII traj
iter Total bad vdW elect nonpolar genBorn frms
ff: 0 112989150.82 4231956.71 108757185.80 152.83 0.00 -144.51 2.31e+08
Starting TNCG minimisation
MIN: Iter = 0 NFunc = 1 E = 112989150.82397 RMSG = 2.3124311e+08
CG: It= 3 ( 0.001)q :-)
LS: i= 1 lhs_f= -63803645 rhs_f= -10000.065
lhs_g= 38145632 rhs_g= 90000586
rel_s= 1 abs_s= 0.049655582
max_d= 0.019324419 i_xyz= 7y
LS: step= 1 it= 1
MIN: Iter = 1 NFunc = 5 E = 49185257.16259 RMSG = 8.8199604e+07
CG: It= 2 (999.999)q :-((
LS: i= 1 lhs_f= -26341933 rhs_f= -4127.2259
lhs_g= 15760242 rhs_g= 37145033
rel_s= 1 abs_s= 0.069221233
max_d= 0.028479989 i_xyz= 46x
LS: step= 1 it= 1
---------------------------------------------------------------------------------
and ultimately, this resulted in .nc entropy being 229.339 cal/mol/K and ASCII entropy being 235.914 cal/mol/K. Fortunately the difference is not big in this instance. But I'm totally surprised by this finding!
------------------------------------------------------------------
Sender:Liao <liaojunzhuo.aliyun.com>
Sent At:2021 Nov. 14 (Sun.) 14:30
Recipient:AMBER Mailing List <amber.ambermd.org>
Subject:[AMBER] Using mmpbsa_py_nabnmode directly
Dear Amber Community,
I'm trying to use mmpbsa_py_nabnmode directly instead of from MMPBSA.py. The reason for this is because I'm trying a 3-trajectory free energy calculation approach. If I use MMPBSA.py, it will calculate 3x3=9 times. Not too much a problem for enthalpies, but entropy will take too long.
Trying to run the program, I get a hint from the terminal saying "Usage: mmpbsa_py_nabnmode {pdb} {prmtop} {maxiter} {drms} {'string of MM options'} {nc/trj}" but I could not successfully fill in all the boxes properly, mainly the 'string of MM options'. Could someone maybe provide or point out a more detailed help page on how to use this program and the syntax? Or more general help on performing 3-trajectory entropy calculations would also be great!
Thanks.
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Received on Sun Nov 14 2021 - 21:30:02 PST
