VMD-L Mailing List

From: Justin Gullingsrud (justinrocks_at_gmail.com)
Date: Tue Mar 22 2005 - 18:09:26 CST

Hi,

You should be able to construct segments with resids up to 9999, so it
sounds like the problem could be that the resid column in water_hex is
misaligned. Make sure that the resid occupies
columns 23-26; otherwise the resid could be clipped when it's read in by psfgen.

Justin

On Tue, 22 Mar 2005 16:19:51 -0500, dimka <newyorkdimka_at_gmail.com> wrote:
> Hello, I'm trying to combine two pdb files, one of them is system.pdf,
> the other is water_box.pdb
>
> system file has my protein; water_box.pdb has 7 segment IDs, each with
> 4939 water molecules. When i run the script (see bellow) the output
> file has all the coordinates from the system.pdb while some waters
> have 0.00 coordinates from water_box.pdb. Only those waters with
> resnum > 999 have 0.000 coordinates, the rest waters are fine.
>
> can anyone please tell me how to fix this or get around it?
>
> I'm using the following tcl script co merge the two files.
> -------------------------------------------------------
> #!/usr/local/bin/vmd
> # join (parts of) protein complex with a membrane
>
> # set echo on for debugging
> echo on
>
> # need psfgen module and topology
> package require psfgen
> topology charmm27.rtf
>
> # load structures
> resetpsf
> readpsf system.psf
> coordpdb system.pdb
> readpsf water_hex.psf
> coordpdb water_hex.pdb
>
> # write temporary structure
> set temp "temp"
> writepsf $temp.psf
> writepdb $temp.pdb
> exit
> -------------------------------------------------
> 

-- 
The spirit of Plato dies hard.  We have been unable to escape the
philosophical tradition that what we can see and measure in the world
is merely the superficial and imperfect representation of an
underlying reality.
                -- S.J. Gould, "The Mismeasure of Man"