VMD-L Mailing List
From: Pawel Kedzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Thu Apr 22 2021 - 10:43:27 CDT
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W dniu 22.04.2021 o 16:37, Jovana Stelkic pisze:
> Pawel, Thank you for the answer and your time. I have checked the
> option that you said but unfortunately it was not the cause of the
> error. I am sending the whole error text (it pops up only while trying
> to use bfee, but not other analysis, and i always first load psf and
> than dcd into same molecule)
Dear Jovana,
I do not have more ideas other than missing coordinates, although the
reason for them being missing may be different than I guessed. I did not
use bfee myself.
> Info) Using plugin namdbin for coordinates from file
> /home/.../Documents/NAMD/pot_lig/output.coor
> Info) Coordinate I/O rate 0.00 frames/sec, 0 MB/sec, 401.8 sec
This message does look suspicious, and for two reasons. Rate of zero
frames may mean that no coordinates were read indeed, but then why did
it take almost 7 minutes? Maybe this file is empty, missing, or it does
not match your PSF file (i.e. it has different number of atoms)? Or
perhaps you read it in wrong format? Namd .coor files may be written as
plain text (basically PDB format) or as binary, on user choice. You are
using the binary reader, but you may try to open the file in a text
editor and see if it is really the binary format.
With regards,
Paweł
>
> measure center: bad weight sum, would cause divide by zero
> measure center: bad weight sum, would cause divide by zero
> while executing
> "measure center $selection1"
> (procedure "check_polar_theta" line 11)
> invoked from within
> "check_polar_theta $psfDir $coorDir $velDir $xscDir"
> (procedure "copy_files" line 14)
> invoked from within
> "copy_files"
> (procedure "::BFEE::generateFiles" line 3)
> invoked from within
> "::BFEE::generateFiles"
> invoked from within
> ".bfee.setupTab.setup.generate invoke "
> invoked from within
> ".bfee.setupTab.setup.generate instate {pressed !disabled} {
> .bfee.setupTab.setup.generate state !pressed;
> .bfee.setupTab.setup.generate invoke } "
> (command bound to event)
>
> and terminal shows:
>
> Info) Using plugin namdbin for coordinates from file
> /home/.../Documents/NAMD/pot_lig/output.coor
> Info) Coordinate I/O rate 0.00 frames/sec, 0 MB/sec, 401.8 sec
> Info) Finished with coordinate file
> /home/jovana/Documents/NAMD/protein/protein_charmm_gui/output.coor
>
>
>
>
> On Thu, 22 Apr 2021 at 15:42, Pawel Kedzierski
> <pawel.kedzierski_at_pwr.edu.pl <mailto:pawel.kedzierski_at_pwr.edu.pl>> wrote:
>
> W dniu 22.04.2021 o 08:25, Jovana Stelkic pisze:
> > Hello,
> > I am into VMD and NAMD for some time now and i'm still learning.
> I did
> > some MD simulations of the protein and ceramide ligands, and I
> did all
> > preparations as it is described in tutorials, I paramatised ligand,
> > generate protein.psf via pgn file as it is written in tutorial,
> made
> > complex via tcl and solvated complex via vmd. I did the simulation
> > with boundaries and PME with cell origin of solvated complex as
> > described in the main NAMD tutorial, i tried with wrap water on and
> > off as well. After simulation I got *.dcd, *.coo, *.vel, *.xsc and
> > *.psf files but when I load *.psf and *.dcd into vmd and enter
> > corresponding files into BFEE and press 'generate input' button it
> > does not generate any of files, just empty folders and it gives
> me an
> > message about error: measure center, bad sum weight would cause
> divide
> > by zero'.
>
> This "measure center" is an internal VMD command used to calculate
> the
> center of your molecule.
>
> Most likely you load PSF and DCD as two separate molecules. Then
> the one
> loaded from PSF has no coordinates and it is the reason why "measure
> center" fails.
>
> Load PSF file first but do not close the "Molecule File Broswer"
> window
> before navigating to and loading DCD file (look at the top entry
> of this
> dialog, it says "Load files for" [selected molecule]).
>
> Cheers,
>
> Pawel
>
> > I tried to add all the hydrogens to the protein also before
> creating
> > psf but no change. Also tried with several pdb files of the same
> > protein from rcsb and with various ligands. I tested plugin with
> > plugin-tutorial example files and it worked. I read similar threads
> > about the same error but can't find the connection. BFEE.tcl script
> > (code) does not contain lines with such error. I would
> appreciate any
> > help about the cause of such error. Bellow is log text of
> creation of
> > protein psf. Thank You.
> >
> > Ceated by CHARMM version 27 1
> > psfgen) aliasing residue HIS to HSE
> > psfgen) aliasing residue ILE atom CD1 to CD
> > psfgen) building segment U
> > psfgen) reading residues from pdb file ncsp.pdb
> > psfgen) extracted 190 residues from pdb file
> > psfgen) Info: generating structure...psfgen) Info: skipping
> improper
> > N-C-CA-HN at beginning of segment.
> > psfgen) Info: skipping conformation C-N-CA-C at beginning of
> segment.
> > psfgen) Info: skipping conformation C-CA-N-HN at beginning of
> segment.
> > psfgen) Info: skipping bond C-N at end of segment.
> > psfgen) Info: skipping improper C-CA-N-O at end of segment.
> > psfgen) Info: skipping conformation CA-C-N-CA at end of segment.
> > psfgen) Info: skipping conformation N-CA-C-O at end of segment.
> > psfgen) Info: skipping conformation N-CA-C-N at end of segment.
> > segment complete.
> > psfgen) reading coordinates from pdb file ncsp.pdb for segment U
> > psfgen) Info: guessing coordinates for 0 atoms (0 non-hydrogen)
> > psfgen) Info: writing pdb file ncs.pdb
> > psfgen) Info: pdb file complete.
> > psfgen) Info: writing psf file ncs.psf
> > psfgen) total of 3048 atoms
> > psfgen) total of 3080 bonds
> > psfgen) total of 5565 angles
> > psfgen) total of 8161 dihedrals
> > psfgen) total of 491 impropers
> > psfgen) total of 0 explicit exclusions
> > psfgen) total of 0 cross-terms
> > psfgen) Info: psf file complete.
> > vmd >
> >
> > Best regards,
> > Jovana
>
>
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