VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Feb 15 2012 - 18:14:24 CST

On Wed, Feb 15, 2012 at 7:11 PM, Aric Newton <agnewton_at_berkeley.edu> wrote:
> Dear John and Axel,
>
> Thank you for your replies and the more detailed info on how the Hbond
> algorithm does what it does.  The naming conventions appear to be key.
> Your tips also suggest I should revisit topotools docs as the guessatoms
> options have been expanded since my last reading.
>
> I can render the Hbonds through the Graphical Representations dialog but
> haven't had luck (yet) with the Analysis> Hydrogen Bonds extension.  5
> minutes after I hit <send> I realized that I have the data file in other
> formats (*.car/ *.mdf) and can convert it to a *.pdb file.  I'll use
> that as a starting point and keep at it.

aric,

it'll be better to generate a .psf file instead of .pdb file
since the .psf doesn't contain coordinates, but the .pdb does.
you usually don't want those "parasitic" coordinates in
your analysis, right?

cheers,
    axel.

>
> Thanks again to you both.
>
> Aric
>
>
> On Wed, 2012-02-15 at 10:13 -0600, John Stone wrote:
>> 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.
>>
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.