VMD-L Mailing List

From: Benjamin Cowen (bjcowen90_at_gmail.com)
Date: Sun Aug 04 2013 - 18:07:39 CDT

Can you think of a more convenient form I should convert a .cif to that
would store coordinates, store cell info, and is something VMD could
interpret? I know I will need to turn autobonds off and then define my own
force field, just trying to minimize the amount of work.

Ben

On Sun, Aug 4, 2013 at 2:21 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Sat, Aug 3, 2013 at 11:07 PM, Benjamin Cowen <bjcowen90_at_gmail.com>
> wrote:
> > Axel,
> >
> > Is there a plugin yet to load cif files directly into VMD? Should I just
>
> no.
>
> > convert .cif to .xyz using another program first, then load into VMD?
>
> something like that. mind you, .xyz doesn't store the cell
> information, so that will have to be entered manually.
>
> > What resulted from
> > http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/10040.html
>
> nothing i know of. lots of people begin something and never get
> anywhere. happened to me a few times, too.
>
> axel.
>
> > 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.
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
>