Dear Amber list,
This is quite a naive question (as I don't usually use MMPBSA.py) - but I
am struggling with how to run MMPBSA.py with a protein-ligand system in
which I also have a non-standard residue in the protein.
I've generated topology files and trajectory files containing the complex
(without solvent), the protein/receptor only (with non-standard residue)
and the ligand only.
The trouble is that - according to the manual - I can only specify a
solvated trajectory file, a receptor one and a ligand one. The complex
trajectory is thus generated by MMPBSA.py, BUT this does not include the
non-standard amino acid (it is not present in _MMPBSA_complex.mdcrd.0 or
_MMPBSA_complex.pdb)
The complex topology I generated and specify in the MMPBSA.py command, does
contain the non-standard amino acid (as it should), and thus the
calculation fails.
How can I make sure the non-standard amino acid is included in the complex
trajectory?
I'm using AmberTools 16.6 at the moment.
example command:
$AMBERHOME/bin/MMPBSA.py -O -sp solvated.top -i mmgbsa.i -cp
strip.solvated.top -rp receptor.top -lp ligand.top -y md.crd -yr rec.nc -yl
lig.nc &
Many thanks,
Marc
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Received on Mon Jun 05 2017 - 08:00:04 PDT
