TCL script for creating PSF and PDB files from Chimera generated protein ligand files

CreatePSF.tcl

## Written by Leela S. Dodda, leela.dodda@yale.edu
##COMMAND TO RUN THE CODE 
##VMD -dispdev text -e CreatePSF.tcl 
mol load pdb protein_clean.pdb 
## Change the pdb file name to one of your choice 
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
topology top_opls_aam.inp 
topology UNK.rtf 
pdbalias residue HIS HSE   
pdbalias residue HID HSD   
pdbalias residue HIP HSP   

segment PROA {
 pdb myfile_frag0.pdb 
}

coordpdb myfile_frag0.pdb PROA 
segment PROB {
 pdb myfile_frag1.pdb
}

coordpdb myfile_frag1.pdb PROB

segment LIGA {
 first none
 last none
 pdb UNK.pdb
}

coordpdb UNK.pdb LIGA 

guesscoord

writepsf complex.psf
writepdb complex.pdb
package require solvate
solvate complex.psf complex.pdb -t 12 -o complex_wb
package require autoionize
autoionize -psf complex_wb.psf -pdb complex_wb.pdb -neutralize -o ionized
exit

VMD -e CreatePSF.tcl