Create PSF file and other things using the following script

MetaDynamics_CreatePSF.tcl

## vmd -dispdev text -e MetaDynamics_CreatePSF.tcl
mol load pdb protein_clean.pdb 
set protein [atomselect top protein]
set chains [lsort -unique [$protein get pfrag]]
foreach chain $chains {
set sel [atomselect top "pfrag $chain"]
$sel writepdb myfile_frag${chain}.pdb
}
### Split the PDB file into segments and then create a over all psf/pdb file
package require psfgen
package require solvate
package require autoionize
topology top_opls_aam.inp 
topology LIG.rtf 
pdbalias residue HIS HSE   
pdbalias residue HID HSD   
pdbalias residue HIP HSP   
#
segment PROA {
 pdb myfile_frag0.pdb 
}
coordpdb myfile_frag0.pdb PROA 
#MAKE SURE YOU GIVE PDB FILE YOU USE HERE IS THE PDB FILE 
segment LIGA {
 first none
 last none
 pdb LIG_final.pdb
}
coordpdb LIG_final.pdb LIGA 
#
guesscoord 
writepsf complex.psf
writepdb complex.pdb
solvate complex.psf complex.pdb -t 12 -o complex_wb
autoionize -psf complex_wb.psf -pdb complex_wb.pdb -neutralize -o ionized
mol load pdb ionized.pdb
[atomselect top "backbone"] set beta 1
[atomselect top "all"] writepdb fixed.pdb
put "Printing Calpha atoms that are \nwithin 5 Angstroms of ligand"
[atomselect top "(name CA) and (within 5 of segname LIGA)"] get serial 
exit