VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Aug 03 2013 - 15:03:40 CDT

On Fri, Aug 2, 2013 at 10:25 PM, Benjamin Cowen <bjcowen90_at_gmail.com> wrote:
> Hello,
>
> I am having an issue regarding bonding.
> This is what I have done:
>
> - Downloaded Y2Ti2O7 .cif file from ICSD database.
> -Converted .cif -> .pdb using OpenBabel
> -Used Avogadro to create supercell

why not use VMD?

> -Saved supercell as .pdb
> -Using topotools on VMD's inorganic builder, I loaded this .pdb file

i don't understand what you mean by this and what this is supposed to do?
topotools and inorganic builder are two separate entities.

> containing supercell

writing out to a .pdb file is effectively undoing the work you
probably did in the previous step, since .pdb files contain no
topology information. this is stored in .psf files for example.

> -I then converted pdb to lammps data file

which will be utterly useless because of the loss of information.

> However, vmd is giving me the below error. I checked and the database stores
> units in Angstroms as I know that could be the cause. Can anyone help me
> figure out this error?

the error message is a result of VMD trying to guess bonding through
heuristics, when there are no bonds present in the file it reads. for
everything but simple organic molecules, these heuristics are often
inaccurate or plain wrong. obviously the latter is the happening in
your case. VMD has a compiled in static limit for the maximum number
of bonds that an atom can have, which is what your file is obviously
overstepping.

there are two major issues with your strategy:
a) .pdb files have very low accuracy on the coordinate data and are
pretty much a bad idea outside of extracting cystal structure data
from the protein data base.
b) you should load your initial coordinates from the command line into
VMD and telling VMD to disable automatic bond detection and then only
generate the topology data (bonds/angles/dihedrals/etc.) that is
required for your force field, and then rather store this topology
information in a .psf or some other file that support topology data

axel

>
> Thanks,
>
> Ben
>
> ERROR) MolAtom 7: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 8: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 9: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 10: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 158: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 160: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 161: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 162: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 163: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 311: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 313: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 314: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 315: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 316: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 464: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 466: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 467: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 468: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 469: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 617: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 619: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 620: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 621: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 622: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 771: Exceeded maximum number of bonds (12).
> ERROR) BaseMolecule: Excessive bonding errors encountered, perhaps atom
> coordinates are in the wrong units?
> ERROR) BaseMolecule: Silencing bonding error messages.
> Info) Using plugin pdb for coordinates from file
> /home/owner/Desktop/Y2Ti2O7_supercell.pdb
> Info) Determining bond structure from distance search ...
> Info) Eliminating bonds duplicated from existing structure...
> Info) Analyzing structure ...
> Info) Atoms: 19125
> Info) Bonds: 43016
> Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> Info) Residues: 321
> Info) Waters: 0
> Warning) Unusual bond between residues: 1 (none) and 3 (protein)
> Warning) Unusual bond between residues: 1 (none) and 3 (protein)
> Warning) Unusual bond between residues: 1 (none) and 3 (protein)
> Warning) Unusual bond between residues: 1 (none) and 3 (protein)
> Warning) Unusual bond between residues: 4 (none) and 282 (protein)
> Warning) Unusual bond between residues: 4 (none) and 282 (protein)
> Warning) Unusual bond between residues: 4 (none) and 282 (protein)
> Warning) Unusual bond between residues: 4 (none) and 279 (protein)
> Warning) Unusual bond between residues: 4 (none) and 279 (protein)
> Warning) Unusual bond between residues: 4 (none) and 279 (protein)
> Warning) Unusual bond between residues: 4 (none) and 285 (protein)
> Warning) Unusual bond between residues: 4 (none) and 285 (protein)
> Warning) Unusual bond between residues: 4 (none) and 285 (protein)
> Warning) Unusual bond between residues: 4 (none) and 287 (protein)
> Warning) Unusual bond between residues: 4 (none) and 287 (protein)
> Warning) Unusual bond between residues: 4 (none) and 287 (protein)
> Info) Segments: 1
> Info) Fragments: 35 Protein: 0 Nucleic: 0
> Info) Finished with coordinate file
> /home/owner/Desktop/Y2Ti2O7_supercell.pdb.
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.