VMD-L Mailing List

From: dimka (newyorkdimka_at_gmail.com)
Date: Tue Mar 22 2005 - 15:19:51 CST

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
-------------------------------------------------