VMD-L Mailing List

From: Anton Arkhipov (anton_at_ks.uiuc.edu)
Date: Wed Nov 05 2008 - 16:16:59 CST

Hi Anirban,

I looked at the files you sent me. The CG Map Tool does not work for
you because there are several things you are doing wrongly. Here are
the problems...

1. Indeed, you need to have the same segname for the CG PDB, all-atom
reference PDB, AND the all-atom PDB you want to map you CG structure
onto. In your files, you didn't have these segnames at all. Note, in
your reference all-atom file, you had several different segnames - one
for the protein, one for one RNA piece, another for the other RNA
piece, and so on. This is not how it is supposed to work. If it is the
whole all-atom PDB file that you are representing by the CG model,
EVERYTHING in the all-atom file should have the same segname,
otherwaise the Map tool will not work properly.

You should have checked the manual for the plugin (http://www.ks.uiuc.edu/Research/vmd/plugins/cgtools/
), where it is written about the mapping: "for two atoms to be
declared identical, segname, resid, and name should match".

2. For some reason, the all-atom file onto which you want to map the
CG structure contains two protein units, instead of one. This is OK in
general, but you need to make sure that the protein unit to which you
are mapping the CG structure has the same segname as that in your CG
PDB and in your all-atom reference file. The other subunit in your all-
atom file for mapping should have a different segname. The most
efficient is, of course, to remove anything unnecessary from your file
for mapping.

3. You have some of the atom names (e.g., name O5*) in your mapping
file, which are different in your reference file. The names such as
O5* come from the crystal structure, but are not recognized by VMD
selections. Apparently, your reference file was obtained using psfgen
(in the AutoPSF plugin). So you have to process your structure for
mapping using psfgen too, like you did for the reference file.
Otherwise, you have different atom names in the two files, which
creates troubles for the mapping tool, and VMD even does not recognize
some of those names when making selections.

So, try to fix the names and segnames, and run the mapping tool again.
It worked for me. Let me know if you have problems.

Also, in the all-atom files you are using (both the reference file and
the file for mapping), you have protein, RNA, water, and other things.
This is a rather strange way to run your coarse-graining. You should
coarse-grain the protein separately. This should not be a problem for
the plugin, though, once all resid's, atom names and segnames are
taken care of properly.

Best,

Anton.

On 5 Nov 2008, at 04:48, Anirban Ghosh wrote:

> Hi ALL,
>
> In the previous post I mentioned that there was some error with
> "segname", while using the CG Map Tool of the new VMD test version.
> However I rectified that by making the segname of the modelled CG
> PDB and the segname of the all-atom PDB, same. But now I am getting
> the following error while I am trying to build the CG model for the
> entire 60 chain protein, using the CG Map Tool:
>
> -------------------------------------------------------------------------------------------------------------
>
> can't read "cg_pos(0)": no such element in array
> can't read "cg_pos(0)": no such element in array
> while executing
> "vecadd $cg_pos($i_CG) [vecscale [lindex $AAmass $i] [lindex $AApos
> $i]"
> (procedure "::cgtools::mapCGMolecule" line 45)
> invoked from within
> "::cgtools::mapCGMolecule foobar $::cggui::currentMapAAMol
> $::cggui::currentMapCGMol $::cggui::currentMapRefMol
> $::cggui::mapOutpdbfile"
> (procedure "::cggui::mapSBExecute" line 19)
> invoked from within
> "::cggui::mapSBExecute"
> invoked from within
> ".cggui.mapSBFrame.applyDB invoke"
> ("uplevel" body line 1)
> invoked from within
> "uplevel #0 [list $w invoke]"
> (procedure "tk::ButtonUp" line 22)
> invoked from within
> "tk::ButtonUp .cggui.mapSBFrame.applyDB
> "
> (command bound to event)
> -------------------------------------------------------------------------------------------------------------------------------------------
>
> Any suggestion to rectify this error is welcome.
>
> Regards,
>
>
>
>
> Anirban Ghosh
> M.Tech Bioinformatics
> University of Hyderabad
>
>
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