VMD-L Mailing List

From: Benjamin Cowen (bjcowen90_at_gmail.com)
Date: Fri Aug 02 2013 - 15:25:37 CDT

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
-Saved supercell as .pdb
-Using topotools on VMD's inorganic builder, I loaded this .pdb file
containing supercell
-I then converted pdb to lammps data file

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?

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.