VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Feb 14 2012 - 15:36:13 CST

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.