Confused with psfgen module of VMD

Question

[Christopher]

I am fairly new to VMD and programming in general. I need to combine two pdb files of subunits into a combined pdb and psf file with both subunits. I used the Namd tutorial and used two pdb files named BChain270VerCTrue.pdb and barn_noH2o_ChainD.pdb and ran this pgn in VMD:

package require psfgen 
topology top_all27_prot_lipid.inp 
pdbalias residue HIS HSE 
pdbalias atom ILE CD1 CD 
segment A {pdb BChain270VerCTrue.pdb} 
segment D {pdb barn_noH2o_ChainD.pdb} 
coordpdb BChain270VerCTrue.pdb A 
coordpdb barn_noH2o_ChainD.pdb D 
guesscoord 
writepdb BarnaseBarnstar270True.pdb 
writepsf BarnaseBarnstar270True.psf`

However, this creates a sort of mangled pdb that has both subunits covalently bonded. How could I fix this?

This is how the two pdb files look when just used separately in VMD:

This is what the code spits out: