From: Benjamin Cowen (bjcowen90_at_gmail.com)
Date: Sat Aug 03 2013 - 16:07:17 CDT

Axel,

Is there a plugin yet to load cif files directly into VMD? Should I just
convert .cif to .xyz using another program first, then load into VMD?

What resulted from
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/10040.html

Thanks for the info on why my method was not successful.

Ben

On Sat, Aug 3, 2013 at 2:03 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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.
>