VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 15 2008 - 10:39:33 CDT

Hi,
  I see that VMD emitted maximum bonding warnings when you loaded
your file. Can you check to see if your coordinate units are correct?
This warning usually comes up with files that store coordinates in
nanometers or some other units rather than angstroms.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jul 14, 2008 at 10:43:43AM -0600, mahesh naalla wrote:
> Hello everyone,
> I am trying to visualise History file produced from simulations run in
> DL_POLY.
> I am loading the molecule on to VMD using file/new molecule and selecting
> file type as
> DLPOLY V2 HISTORY.
> It is giving me the perspective image which is very unclear but when I
> change the option
> in display to orthographic, image is very clear.
> But what my problem is it is just giving me the atoms no clear bonding
> between them.
> All the atoms were displayed as dots and few lines.
> As soon as I load the file following messages are resulting.
>
>
>
> Info) VMD for WIN32, version 1.8.6 (April 7, 2007)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Free system memory: 888MB (43%)
> Info) OpenGL renderer: Intel 965/963 Graphics Media Accelerator
> Info) Features: STENCIL MDE CVA MTX PP
> Info) GLSL rendering mode is NOT available.
> Info) Textures: 2-D (2048x2048), 3-D (128x128x128), Multitexture (8)
> Info) Spaceball driver not installed. Spaceball interface disabled.
> Info) No joysticks found. Joystick interface disabled.
> Found 62 plugins or data handlers in directory
> 'C:/Program Files/University of Illinois/VMD/plugins/WIN32/molfile'.
> vmd > Info) Using plugin dlpolyhist for structure file
> C:/Users/mahesh/Desktop/H
> ISTORY1.txt
> Info) Using plugin dlpolyhist for coordinates from file
> C:/Users/mahesh/Desktop/
> HISTORY1.txt
> dlpoly timestep) converting DLPOLY periodic cell data
> Info) Determining bond structure from distance search ...
> ERROR) MolAtom 1792: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 2081: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 2096: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 1609: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 1621: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 1635: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 1646: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 1658: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 1671: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 1684: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 1696: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 1704: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 1716: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 1730: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 1741: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 1609: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 1621: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 1635: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 1646: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 1658: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 1671: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 1684: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 1696: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 1704: Exceeded maximum number of bonds (12).
> ERROR) MolAtom 1716: Exceeded maximum number of bonds (12).
> ERROR) BaseMolecule: Excessive bonding errors encountered, perhaps atom
> coordina
> tes are in the wrong units?
> ERROR) BaseMolecule: Silencing bonding error messages.
> Info) Analyzing structure ...
> Info) Atoms: 3407
> Info) Bonds: 4778
> Info) Residues: 1267
> Info) Waters: 0
> Info) Segments: 1
> Info) Fragments: 1267 Protein: 0 Nucleic: 0
> Info) Finished with coordinate file C:/Users/mahesh/Desktop/HISTORY1.txt.
>
> I would immensely appreciate any response.
> Thanks
> Mahesh Naalla 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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