VMD-L Mailing List

From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Thu Jun 05 2014 - 11:55:56 CDT

Hi Diego,

In the code that you presented, you make modifications to VMD's molecule #0. If you load trajectory afterwards, it has different number. So, you just need to adjust your script so that it works with the right thing, e.g.:

set MOL [mol load psf "psfFile.psf"]
mol addfile dcdFile.dcd waitfor all $MOL

mol modstyle 0 $MOL NewCartoon
mol modcolor 0 $MOL ColorID 3

.. and so on.

Maxim

On Jun 5, 2014, at 11:34 AM, Diego Granados <webbynator42_at_gmail.com> wrote:

> Hi !
>
> I made a small script in order to visualize charmm predicted hbonds through a trajectory with vmd. The output of the script is a tcl file which makes a visual representation for each hydrogen bond. When i use it with a single pdb it works without any trouble but when i try to do the same for a trajectory it doesn't work. This is an excerpt of the code:
>
> mol load psf /Volumes/nut/diego/secar_nonamero/archivos/nonamero_proteina.psf
>
>
> mol addfile /Volumes/nut/diego/secar_nonamero/trayectorias/step7_all_proteina_str10.dcd dcd 0
>
> mol modstyle 0 0 NewCartoon
>
> mol modcolor 0 0 ColorID 3
>
> mol selection (segid PROA and resid 46 and type HN) or (segid PROA and resid 78 and type O)
>
> mol addrep 0
>
> mol modstyle 1 0 VDW
>
> mol modcolor 1 0 ColorID 1
>
> mol selection (segid PROA and resid 72 and type HN) or (segid PROA and resid 52 and type O)
>
> mol addrep 0
>
> mol modstyle 2 0 VDW
>
> mol modcolor 2 0 ColorID 1
>
>
>
> Does anyone have any clue about the trouble?
>
> If you have any trouble in order to understand my message don't hesitate in telling me.
>
> Thank's a lot!
>
> Diego.
>