TCL Write a pdb

vm_writepdb.tcl

#################################################
## TCL script to write a pdb of initial structure
## Kevin Apr 2014
## Usage  vmd -dispdev text -e <tcl>
## Output  a pdb file
#################################################

mol new ../../../ionized.pdb
set sel [atomselect top protein]
$sel writepdb initial.pdb
mol delete all

vm_autopsf.tcl

mol new ../../../ionized.pdb
set sel [atomselect top protein]
$sel writepdb first.pdb
mol delete all

package require autopsf
mol new first.pdb
autopsf -mol top -top top_all36_prot.rtf