I'm trying Amberlite for the first time, on a set of data for which I've run a 3-point MMGBSA pairwise energy decomposition, reporting 2 residues specifically.
This is my call:
pymdpbsa --proj=cpd4dec --traj=cpd4apr.dcd --cprm=cpd4apr.prmtop --lprm=cpd4a.prmtop --rprm=ns.prmtop --lig=FLV --start=3000 --stop=5000 --step=1000 --solv=1
& these are my errors:
......
addstrand: strand A already in mol
addstrand: strand A already in mol
failure in molsurf
Traceback (most recent call last):
File "/usr/amber11/AmberTools/amberlite/bin/pymdpbsa", line 772, in ?
opt.start, opt.stop, opt.step, gb, sa)
File "/usr/amber11/AmberTools/amberlite/bin/pymdpbsa", line 88, in nrgtable_gb
etot, ebat, evdw, ecoul, egb, sasa = ffgbsa(prmtop, pdbfile, gb, sa)
File "/usr/amber11/AmberTools/amberlite/bin/pymdpbsa", line 264, in ffgbsa
etot = etot + sasa
UnboundLocalError: local variable 'etot' referenced before assignment
Thanks for your help!
Irene Newhouse
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Received on Tue Aug 16 2011 - 14:00:02 PDT
