VMD-L Mailing List

From: Aric Newton (agnewton_at_berkeley.edu)
Date: Tue Feb 14 2012 - 14:22:27 CST

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.

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?

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 %