Dear Amber,
Since we would like to strip any atoms in the area of larger than 20 A of
the ligand in entropy calculation to save computational costs, we use the
*strip_mask* flag in MMPBSA.py
Input file running entropy
&general
keep_files=2, strip_mask=:ligand<:20,
/
&nmode
nminterval=500,
nmode_igb=1,
nmode_istrng=0.1,
/
MMPBSA.py.MPI -O -i entropy_RESP_6000ps.in -o complex_entropy.dat -sp
solvated_complex.prmtop -cp complex.prmtop -rp receptor.prmtop -lp
ligand.prmtop -eo entropy.csv -y solvated_complex.mdcrd
However, the following error message, *"Error: No reference set for
[solvated_complex.prmtop], cannot select by distance."* keeps poping out
and failed the calculation.
If we try to take off "-sp solvated_complex.prmtop", as following, the
same error message still pops out.
MMPBSA.py.MPI -O -i entropy_RESP_6000ps.in -o complex_entropy.dat -cp
complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -eo entropy.csv -y
solvated_complex.mdcrd
Error: No reference set for *[complex.prmtop]*, cannot select by distance.
We have also try strip_mask=:ligand<:20, strip_mask=':ligand<:20',
strip_mask=":ligand<:20", and none of them works.
All the above simulations will be terminated in the middle/after cpptraj
process of MD trajectories and generate the following files.
406847488 Nov 25 14:10 _MMPBSA_complex.mdcrd.0 (0-47 for 48 frames)
364904448 Nov 25 14:10 _MMPBSA_ligand.mdcrd.0 (0-47 for 48 frames)
404750336 Nov 25 14:10 _MMPBSA_receptor.mdcrd.0 (0-47 for 48 frames)
Could any guru kindly offers some comments? Thanks.
Cheers,
Henry
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Received on Mon Nov 25 2013 - 12:30:04 PST
