VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Dec 12 2020 - 10:39:41 CST

Hi all
The vmd interface to ProDy has problems with psf/dcd files limited to the
quantum mechanical part of QMMM simulations (QMonly.dcd files) carried out
with NAMD/ORCA. No problems with psf/dcd MD files for the same (whole)
system, I could generate nmd files and plots. Thanks for advice
francesco pietra
 The error log reads;
>
>
> Traceback (most recent call last):
> File "/opt/anaconda3/bin/prody", line 11, in <module>
> sys.exit(prody_main())
> File
> "/opt/anaconda3/lib/python3.7/site-packages/prody/apps/prody_apps/__init__.py",
> line 53, in prody_main
> namespace.func(namespace)
> File
> "/opt/anaconda3/lib/python3.7/site-packages/prody/apps/prody_apps/prody_anm.py",
> line 283, in <lambda>
> **ns.__dict__))
> File
> "/opt/anaconda3/lib/python3.7/site-packages/prody/apps/prody_apps/prody_anm.py",
> line 75, in prody_anm
> anm.calcModes(nmodes)
> File "/opt/anaconda3/lib/python3.7/site-packages/prody/dynamics/anm.py",
> line 219, in calcModes
> turbo=turbo, expct_n_zeros=6)
> File
> "/opt/anaconda3/lib/python3.7/site-packages/prody/utilities/eigtools.py",
> line 88, in solveEig
> values, vectors = _eigh(M, eigvals, turbo)
> File
> "/opt/anaconda3/lib/python3.7/site-packages/prody/utilities/eigtools.py",
> line 41, in _eigh
> values, vectors = linalg.eigh(M, turbo=turbo, eigvals=eigvals)
> File
> "/opt/anaconda3/lib/python3.7/site-packages/scipy/linalg/decomp.py", line
> 488, in eigh
> 'start={}, end={} is given'.format(n-1, lo, hi))
> ValueError: Requested eigenvalue indices are not valid. Valid range is [0,
> 14] and start <= end, but start=0, end=15 is given
> Traceback (most recent call last):
> File "/opt/anaconda3/bin/prody", line 11, in <module>
> sys.exit(prody_main())
> File
> "/opt/anaconda3/lib/python3.7/site-packages/prody/apps/prody_apps/__init__.py",
> line 53, in prody_main
> namespace.func(namespace)
> File
> "/opt/anaconda3/lib/python3.7/site-packages/prody/apps/prody_apps/prody_anm.py",
> line 283, in <lambda>
> **ns.__dict__))
> File
> "/opt/anaconda3/lib/python3.7/site-packages/prody/apps/prody_apps/prody_anm.py",
> line 75, in prody_anm
> anm.calcModes(nmodes)
> File "/opt/anaconda3/lib/python3.7/site-packages/prody/dynamics/anm.py",
> line 219, in calcModes
> turbo=turbo, expct_n_zeros=6)
> File
> "/opt/anaconda3/lib/python3.7/site-packages/prody/utilities/eigtools.py",
> line 88, in solveEig
> values, vectors = _eigh(M, eigvals, turbo)
> File
> "/opt/anaconda3/lib/python3.7/site-packages/prody/utilities/eigtools.py",
> line 41, in _eigh
> values, vectors = linalg.eigh(M, turbo=turbo, eigvals=eigvals)
> File
> "/opt/anaconda3/lib/python3.7/site-packages/scipy/linalg/decomp.py", line
> 488, in eigh
> 'start={}, end={} is given'.format(n-1, lo, hi))
> ValueError: Requested eigenvalue indices are not valid. Valid range is [0,
> 14] and start <= end, but start=0, end=15 is given
> while executing
> "exec $::NMWiz::pybin $::NMWiz::prody anm --quiet -s $selstr {*}$args
> "$pdbfn""
> (procedure "::NMWiz::prodySubmitANMjob" line 42)
> invoked from within
> "::NMWiz::prodySubmitANMjob"
> (procedure "::NMWiz::prodySubmitJob" line 22)
> invoked from within
> "::NMWiz::prodySubmitJob"
> invoked from within
> ".nmwizprody.submitFrame.prodySubmit invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 22)
> invoked from within
> "tk::ButtonUp .nmwizprody.submitFrame.prodySubmit"
> (command bound to event)
>