VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Nov 29 2010 - 10:32:03 CST

Hi,
  It seems that the PSF file generated by top2psf didn't contain
any bonds, which could cause problems with any analysis scripts
that need that information. I'd suggest that you look into why
there are no bonds defined in the PSF that top2psf created.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Nov 27, 2010 at 03:45:37PM +0330, leila karami wrote:
> 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 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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