VMD-L Mailing List

From: Jovana Stelkic (jovanastelkic_at_gmail.com)
Date: Thu Apr 22 2021 - 01:25:22 CDT

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'. 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