From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Aug 04 2013 - 23:20:35 CDT

On Mon, Aug 5, 2013 at 1:07 AM, Benjamin Cowen <bjcowen90_at_gmail.com> wrote:
> 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.

for something that you are not doing a lot of times, it is not worth
to spend much effort on minimizing the amount of work. setting the
cell parameters manually is easy and the whole process can be scripted
(which is highly recommended to make it reproducible).

axel.

>
> 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.
>
>

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