VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 15 2012 - 10:13:18 CST

Hi,
  I thought I'd chime in and amplify Axel's comment regarding atom
names/types. The hbond visualization and analysis functions of VMD
look for atom names/types that they recognize, if you're using
a naming scheme that VMD doesn't understand, then it won't be able to
do the visualization/analysis you want. The simplest way to fix this
is to rename the atoms, and then do a "mol reanalyze" so VMD re-tags
the atoms it is able to recognize.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Feb 14, 2012 at 04:36:13PM -0500, Axel Kohlmeyer wrote:
> dear aric,
>
> On Tue, Feb 14, 2012 at 3:22 PM, Aric Newton <agnewton_at_berkeley.edu> wrote:
> > Dear VMD users,
> >
> > I am trying to use the Hydrogen Bonds extension to assess the hydrogen
> > bonding of a hydroxyl anion in SPC/E water.  I have run the simulation
> > in LAMMPS and am loading it into VMD using the sequence 1) topotools
> > readlammpsdata <file>; 2) topo guessatom element mass; and 3) loading
> > the lammps trajectory (*.atom format) into the molecule.
>
> better yet. try:
>
> topo guessatom lammps data
>
> to import/reconstruct as much VMD information from the
> LAMMPS data file as possible. that should set atom names
> as well.
>
>
> > The Hydrogen Bonds extension executes with what appears to be valid
> > input data, but returns a "Warning) multiplot: Data vector empty,
> > ignoring plot!"  Obviously, the output is not reliable.  However, there
> > is no overlap in atom selections.  Each water molecule has a unique
> > resid but they all have the same molecule id: 0 and chain: X.  I have
> > provided the Hydrogen Bonding scripts parameters from the Terminal
> > window below and the output from a TkConsole command line attempt as
> > well. I've looked through the archive to try to see if there is
> > something obvious I am missing, but I have yet to locate it.
> >
> > I have used the brH.pdb file in the /protein directory distributed with
> > VMD to test if the problem is user-error or something else.  The
> > Graphical Representations> Drawing Method> Hbonds technique depicts
> > H-bonds in the brH.pdb model. Although,the TkConsole indicates that
> > there are 441 hbonds found and provides a list when I use the Hydrogen
> > Bonds Extension, the "Warning) muliplot: Data vector empty, ignoring
> > plot!" message persists and no graph is generated.
> >
> > I've tried this with both v.1.9 and the new v.1.9.1 of VMD on Ubuntu
> > 10.04 LTS and v.1.9 on Mac OS X 10.7.  Are hydrogen bonds absent because
> > there are no "explicit" hydrogen atoms in the structure?  The "topo
> > guessatom element mass" correctly assigns the elements and I can color
> > the model (correctly) by element.  But there is no indication what the
> > element is when I pick the atoms in the Display (names=types).  Where is
> > this info stored and how can I get the Hbonds tools to see it?
>
> each atom has various properties (name, type, element, mass, charge,
> x, y, z, resid, residue, resname, fragment, index, serial, ...).
> those are stored with the molecule topology information.
>
> this can be accessed from script level with atom selections.
> e.g. to give all atoms of type 1 the name "OW" you would do
>
> set sel [atomselect top {type 1}]
> $sel set name OW
> $sel delete
>
> and so on. the hbond plugin assumes a combination of
> PDB/NAMD/CHARMM/Amber naming conventions to
> identify hydrogens, and hbond donors and acceptors.
> this may not be 100% consistent with the Hbond representation.
>
> so if, using the more extended: topo guessatoms lammps data
> doesn't help to get you up to speed, you can just write a little
> script that renames the atoms by lammps type number to something
> that will be properly recognized by VMD and then write it
> out as a .psf file for later re-use.
>
> due to the way, how lammps strips of all information about
> conventional naming from its input, you have to resolve to
> these tricks. to do analysis.
>
> life is tough. :-(
>
> cheers,
> axel.
>
>
> >
> >
> >
> > Sorry if I have overloaded you with diagnostic info but I am stumped.
> > Thank you for reading.
> >
> > Sincerely,
> >
> > Aric
> >
> >
> >
> > Parameters used in the calculation of hydrogen bonds:
> > - Atomselection 1: type 3 4
> > - Atomselection 2: type 1 2
> > - Update selections every frame: yes
> > - Initial frame: 0
> > - Frame step: 1
> > - Final frame: 5001
> > - Donor-Acceptor distance: 3.0
> > - Angle cutoff: 20
> > - Type: none
> > - Write a file with H bond/frame data: no
> >
> >
> > Found 0 hbonds.
> > donor            acceptor        occupancy
> > Warning) multiplot: Data vector empty, ignoring plot!
> >
> > Alternate TkConsole output type 1 and type 2 are O(water) and H(water),
> > respectively.
> > Main console display active (Tcl8.5.6 / Tk8.5.6)
> > (NPT_iso500ps) 1 % set sel1 [atomselect top "type 1"]
> > atomselect20
> >>Main< (NPT_iso500ps) 2 % set sel2 [atomselect top "type 2"]
> > atomselect21
> >>Main< (NPT_iso500ps) 3 % measure hbonds 3.5 20 $sel2 $sel1
> > {} {} {}
> >>Main< (NPT_iso500ps) 4 %
> >
> >
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com  http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA. 

-- 
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