VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Fri Sep 17 2004 - 01:16:45 CDT

On Thu, 16 Sep 2004, Alicia Hopkins wrote:

hello alicia,

AH> Thanks to everyone for their suggestions. However, these are my results
AH> from the following code:
AH>
AH>
AH> [root_at_spock root]# ssh -l hopkins_at_magnet.fsu.edu
AH> Usage: ssh [options] host [command]

i suppose that has got nothing to do with it.
but just for the record. it is either
'ssh -l hopkins magnet.fsu.edu'
or 'ssh hopkins_at_magnet.fsu.edu'

hence the error message.

[...]

ok, now for the vmd script code. that seems
perfectly ok, so there must be something
wrong with whitespace or linewraps.

just for demonstration purposes a log
of a session with vmd version 1.8.2 on
my linux machine:

[8|7:59]~/cluster/prak/unit-7> vmd -dispdev text
Info) VMD for LINUX, version 1.8.2 (December 4, 2003)
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) Multithreading available, 1 CPU detected.
vmd > mol new GEOMETRY.xyz
Info) Using plugin xyz for structure file GEOMETRY.xyz
Info) Using plugin xyz for coordinates from file GEOMETRY.xyz
Info) Determining bond structure from distance search ...
Info) Analyzing structure ...
Info) Atoms: 100
Info) Residues: 33
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 33 Protein: 0 Nucleic: 0
0
Info) Finished with coordinate file GEOMETRY.xyz.
vmd > set reference_sel [atomselect 0 all]
atomselect0
vmd > set cutoff 5
5
vmd > set angle 45
45
vmd > set hblist [measure hbonds $cutoff $angle $reference_sel]
{25 9 6 30 7 9 23 27 23 9 14 11 11 16 31 31 6 13 23 12 12 23 0 2 26 14 28
0 13 0 26 10 24 14 24 5 24 26 26 0 28 16 16 16 20 20 29 16 0 32 3 21 17 5
5 5 17 17} {30 25 22 23 6 27 9 4 27 14 9 14 28 11 6 8 13 6 6 8 31 31 8 13
2 2 2 2 3 26 29 26 4 24 20 12 10 12 24 12 14 14 20 28 10 15 21 10 1 0 32
32 32 10 17 32 10 15} {83 51 46 93 48 52 79 88 79 52 62 56 56 66 96 95 45
59 80 57 57 80 33 37 85 61 89 34 60 34 85 53 81 62 82 43 82 86 86 34 89 66
65 66 73 73 75 65 33 99 39 98 68 44 44 44 67 67}
vmd > puts "there are [llength [lindex $hblist 0]] hydrogen bonds"
there are 58 hydrogen bonds
vmd > quit
Info) VMD for LINUX, version 1.8.2 (December 4, 2003)
Info) Exiting normally.

so it _does_ work. but it seems, that on your machine
the commands were not executed individually or there
was some extra code in the measure line, that is not
visible here, since the first three steps seem
to work the same.

best regards,
        axel kohlmeyer.

AH>
AH> set reference_sel [atomselect 0 all]
AH>
AH> set cutoff 5
AH> set angle 45
AH> measure hbonds $cutoff $angle $reference_sel
AH>
AH>
AH> The results are:
AH>
AH> vmd > Type 'measure' for summary of usage
AH>
AH> atomselect4
AH> 5
AH> 45
AH> {} {} {}
AH>
AH>
AH> HELP!
AH>
AH> Alicia C. Hopkins
AH> CIMAR / National High Magnetic Field Laboratory
AH> 1800 East Paul Dirac Drive
AH> Tallahassee, Florida 32310
AH> Phone: 850-644-1309
AH> Fax: 850-644-1366
AH> ahopkins_at_chem.fsu.edu
AH>
AH> 

-- 
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Dr. Axel Kohlmeyer                        e-mail: axel.kohlmeyer_at_rub.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
=======================================================================