VMD-L Mailing List

From: mahesh naalla (naallamahesh_at_gmail.com)
Date: Mon Jul 14 2008 - 11:43:43 CDT

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