Confused with psfgen module of VMD

Confused with psfgen module of VMD

0

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:
Separate

This is what the code spits out:

mangled


bioinformatics


protein


files


database


vmd

• 11 views

Read more here: Source link