Confused with psfgen module of VMD

Question

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:

Answer 1

Barnase and barstar are the extracellular ribonuclease and its intracellular inhibitor produced by Bacillus amyloliquefaciens. These two proteins have strong binding energy therefore frequently used for studying protein-protein interaction. To simulate this interaction in silico, We need a proper 1) Forced field, 2) Topology files, and 3) Molecular Dynamic packages like NAMD, Gromacs, or Amber. Plus little bitty understanding of the PDB file format and Structural Biology, and Python or Bash scripting skills.

To generate a topology file one has to generate each component separately, if PDB file has two chains then one has to separate them. However, when we have to put them back we have to follow PDB file format rules. (details can be found at https://www.wwpdb.org/documentation/file-format).

PDB format is composed of many columns but the first column contains the atom information like ATOM, HETATOM, or TER. The last TER designates termination of one chain, without it some software considers them as a single chain like your case.

Make sure two chains are separated TER. you can use a simple text editor to put.