VMD-L Mailing List

From: Alexandre A. Vakhrouchev (makaveli.lcf_at_gmail.com)
Date: Sun May 11 2008 - 11:20:47 CDT

Hi all! Thanks for your response.

I load data from PSF file and than add coordinates from PDB file.
Perhaps I should describe it to be clear. It contains water made by
'solute' command and with some molecules been removed. It also
contains CNT atoms, which I have made by my own script. It builds
multi wall nanotubes, adding corresponding residues to topology files
to be later associated with water fragment.

When I load system into VMD 1.8.6 I've got following message:

ERROR) BaseMolecule: Cannot add atom; namelist index value to large/
ERROR) Recompile VMD with larger index types.
ERROR) Atom namelist index values at time of overflow:
ERROR) nameindex: 32768
 etc. All other values are 0.

As John have already said the unusual part is connected with CA atoms
in carbon nanotube residue. I built it by myself giving all atoms
unique names in form A, B,...,Z, AA, AB, ..., AZ and so on to use
them in 'coord' command of psfgen. I didn't split tube into segments,
that is why there is 202176 atoms of CNT with unique names. Here is a
part of PSF file corresponding to CNT:

   26932 NT 0 C VVNB CA 0.000000 12.0110 0
   26933 NT 0 C WVNB CA 0.000000 12.0110 0
   26934 NT 0 C XVNB CA 0.000000 12.0110 0
   26935 NT 0 C YVNB CA 0.000000 12.0110 0
   26936 NT 0 C ZVNB CA 0.000000 12.0110 0
   26937 NT 0 C AWNB CA 0.000000 12.0110 0
   26938 NT 0 C BWNB CA 0.000000 12.0110 0

VMD 1.8.5 works properly with this PSF/PDB files and '[atomselect top
"type CA"] get name' reads atom names. I was surprised that 1.8.6
could not open it.

Waiting for your advice. 

-- 
Best regards,
Dr. Alexander Vakhrushev
Institute of Applied Mechanics
Dep. of Mech. and Phys.-Chem.
of heterogeneous mediums
UB of Russian Academy of Sciences
34 T. Baramzinoy St.
Izhevsk, Russia 426067