VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Dec 12 2020 - 11:52:57 CST

Francesco,
  I would suggest reporting this issue to the Bahar lab who are
the main developers of both NMWiz and ProDy:
  http://prody.csb.pitt.edu/index.html
  http://prody.csb.pitt.edu/nmwiz/

Best regards,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Dec 12, 2020 at 05:39:41PM +0100, Francesco Pietra wrote:
> 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)
> > 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/