From: Pawel Kedzierski (
Date: Thu Apr 22 2021 - 08:42:25 CDT

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]).



> 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