From: leila karami (karami.leila1_at_gmail.com)
Date: Sat Nov 27 2010 - 06:15:37 CST

Hi VMD users

I want to know the percentage of existence of each water mediated hydrogen
bonds between protein and dna during my trajectory.
in gromacs mailing list, Tim Causgrove offered me to use bridging_waters.tcl
in VMD.

is it true?

when I used top2psf.pl in linux for obtaining of psf file,

./top2psf.pl -P comeq.pdb -o comp.psf

converting from PDB........ comeq.pdb

psf_res_offset............. 0

reading input files........
DEBUG - starttop........... 0
DEBUG - finishtop.......... 24085
DEBUG - number of atoms.... 24085
DEBUG - number of bonds.... -24085
input files read...........

converting................. done
last atom read............. 24085 HW2
from residue............... 7492 SOL

when I load the psf file in vmd, I got the following:

psfplugin> WARNING: no bond defined in PSF file.
psfplugin> WARNING: no angles defined in PSF file.
psfplugin> WARNING: no dihedrals defined in PSF file.
psfplugin> WARNING: no impropers defined in PSF file.
psfplugin> no cross-terms defined in PSF file.

first of my psf file is as follows:

PSF
       4 !NTITLE
 REMARKS TOPOLOGY CREATED BY PERL SCRIPT (MARC BAADEN)
 REMARKS contact baaden smplinux.de

   24099 !NATOM
       1 MAIN 1 NGL N 1.0000000000 1.0000000000
       2 MAIN 1 NGL H1 1.0000000000 1.0000000000
       3 MAIN 1 NGL H2 1.0000000000 1.0000000000
       4 MAIN 1 NGL H3 1.0000000000 1.0000000000
       5 MAIN 1 NGL CA 1.0000000000 1.0000000000
       6 MAIN 1 NGL HA1 1.0000000000 1.0000000000
       7 MAIN 1 NGL HA2 1.0000000000 1.0000000000
       8 MAIN 1 NGL C 1.0000000000 1.0000000000
       9 MAIN 1 NGL O 1.0000000000 1.0000000000
      10 MAIN 2 LYP N 1.0000000000 1.0000000000
      11 MAIN 2 LYP H 1.0000000000 1.0000000000
      12 MAIN 2 LYP CA 1.0000000000 1.0000000000
      13 MAIN 2 LYP HA 1.0000000000 1.0000000000
      14 MAIN 2 LYP CB 1.0000000000 1.0000000000
      15 MAIN 2 LYP HB1 1.0000000000 1.0000000000
      16 MAIN 2 LYP HB2 1.0000000000 1.0000000000
      17 MAIN 2 LYP CG 1.0000000000 1.0000000000
      18 MAIN 2 LYP HG1 1.0000000000 1.0000000000
      19 MAIN 2 LYP HG2 1.0000000000 1.0000000000
      20 MAIN 2 LYP CD 1.0000000000 1.0000000000
      21 MAIN 2 LYP HD1 1.0000000000 1.0000000000
      22 MAIN 2 LYP HD2 1.0000000000 1.0000000000
      23 MAIN 2 LYP CE 1.0000000000 1.0000000000
      24 MAIN 2 LYP HE1 1.0000000000 1.0000000000
      25 MAIN 2 LYP HE2 1.0000000000 1.0000000000
      26 MAIN 2 LYP NZ 1.0000000000 1.0000000000
      27 MAIN 2 LYP HZ1 1.0000000000 1.0000000000
      28 MAIN 2 LYP HZ2 1.0000000000 1.0000000000
      29 MAIN 2 LYP HZ3 1.0000000000 1.0000000000

is problem in my psf file?

when I used source bridging_waters.tcl in VMD TkConsole, no output was
obtained.
why? Am I doing it incorrect?

In bridging_waters.tcl there is a example section as follows:

Example:
# <pre>
# mol load psf er-ere.psf pdb er-ere.pdb -1-
# # start the bridge calculations
# start_bridging -2-
# # however, one frame has already been read, so do its calculations
# # by hand
# calc_bridging -3-
# # read the rest of the frames (the selections are automatically computed)
# animate read dcd dyn100frames.DCD -4-

Is final output file dyn100frames.DCD?

Should I use each of 1, 2, 3 and 4 separately in VMD TkConsole?

I'm beginner in using tcl scripts in VMD.

please explain more about it.

-- 
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group