VMD-L Mailing List

From: Jovana Stelkic (jovanastelkic_at_gmail.com)
Date: Thu Apr 22 2021 - 13:34:48 CDT

Thank you for the explanation. I will study more that part! As I said I am
still learning and have a lot of questions, first I taught that bad psf
file was cause so I tried to generate several psf from different pdb files,
with added hydrogens prior or without so that progra doesn't have to quess
much about coordinates.
Thank You very much I will work on it

Best Regards,
Jovana

On Thu, 22 Apr 2021, 20:00 Axel Kohlmeyer, <akohlmey_at_gmail.com> wrote:

> The error message "measure center, bad sum weight would cause divide by
> zero" can *only* happen, if your atoms have no masses associated with them.
> That in turn is usually the consequence of not reading your trajectory
> data correctly or using files that are missing this information or are not
> correctly formatted.
> As already noted, if you have .psf and .dcd files you *must* load the .psf
> file first and *then* load the .dcd file(s) into the *same* "molecule" that
> was created in VMD when loading the .psf file. The .psf and .dcd files have
> to match, i.e. contain the same atoms. But since .dcd files have no other
> information than the coordinates and the simulation box dimensions, it can
> only check for consistency outside of the number of atoms and it cannot be
> used for analysis on its own, since there is no required information about
> atom types, names, residues etc. included. You cannot expect an add-on
> script to work correctly if you do not provide the required information.
>
> Axel.
>
> On Thu, Apr 22, 2021 at 3:04 AM Jovana Stelkic <jovanastelkic_at_gmail.com>
> wrote:
>
>> 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
>>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!sGnjST8UJpVSZODO3bcpPu0ud58TcgWq17hO6HgpH1s69b23fB15eXx6pdT_kR1msA$
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>