Hi all,
I am trying to compute the entropy of ligand-receptor complex with normal mode calculations (Amber14). When trying to do so, I encountered the followings (See attached error log and csh command):
/*/bin/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topo
logy 0 has IFBOX == 0
warn('Solvated topology %s has IFBOX == 0' % ifbox)
/*/bin/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topo
logy 0 has IFBOX == 0
warn('Solvated topology %s has IFBOX == 0' % ifbox)
/*/bin/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topo
logy 0 has IFBOX == 0
warn('Solvated topology %s has IFBOX == 0' % ifbox)
/*/bin/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topo
logy 0 has IFBOX == 0
warn('Solvated topology %s has IFBOX == 0' % ifbox)
/*/bin/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topo
logy 0 has IFBOX == 0
warn('Solvated topology %s has IFBOX == 0' % ifbox)
/*/bin/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topo
logy 0 has IFBOX == 0
warn('Solvated topology %s has IFBOX == 0' % ifbox)
/*/bin/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topo
logy 0 has IFBOX == 0
warn('Solvated topology %s has IFBOX == 0' % ifbox)
/*/bin/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topo
logy 0 has IFBOX == 0
warn('Solvated topology %s has IFBOX == 0' % ifbox)
/*/MMPBSA_mods/make_trajs.py:631: UserWarning: Solvated topo
logy 0 has IFBOX == 0
warn('Solvated topology %s has IFBOX == 0' % ifbox)
Error: Could not determine trajectory _MMPBSA_complex.mdcrd.0 format.
Error: Could not set up input trajectory '_MMPBSA_complex.mdcrd.0'.
File "/*/bin/MMPBSA.py", line 95, in <module>
app.file_setup()
File "/*/bin/MMPBSA_mods/main.py", line 156, in file_setup
self.mpi_size, str(external_progs['cpptraj']), self.pre)
File "/*/bin/MMPBSA_mods/make_trajs.py", line 216, in make_tra
jectories
(trj_suffix, i) for i in range(size)], cpptraj)
File "/*/bin/MMPBSA_mods/make_trajs.py", line 467, in __init__
self.Query()
File "/*/bin/MMPBSA_mods/make_trajs.py", line 602, in Query
raise TrajError('%s failed when querying %s' % (self.exe, traj))
TrajError: /*/bin/cpptraj failed when querying _MMPBSA_complex.m
dcrd.0
Exiting. All files have been retained.
Error: Could not determine trajectory _MMPBSA_complex.mdcrd.0 format.
Error: Could not set up input trajectory '_MMPBSA_complex.mdcrd.0'.
File "/*/bin/MMPBSA.py", line 95, in <module>
app.file_setup()
File "/*/bin/MMPBSA_mods/main.py", line 156, in file_setup
self.mpi_size, str(external_progs['cpptraj']), self.pre)
File "/*/bin/MMPBSA_mods/make_trajs.py", line 216, in make_tra
Would appreciate if I can be assisted, your help is appreciated.
-Sook Wong
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Received on Fri Nov 14 2014 - 11:00:02 PST
