如何在pdb文件中添加链、残基和原子？

Question

我想用OpenMM添加一个包含所有残基和每个残基一个碳α原子的链。这里可以使用实例的链接openMM documentation。目前，我的pdb文件pdb file中有一个链。以下是我尝试过的：

from simtk.openmm.app import *
from simtk.openmm import *
from simtk.unit import *
import numpy as np
import mdtraj as md

# Here I remove all other atoms except carbon-alpha and stored them in a new file 'CA_only.pdb'
main_pdb = md.load_pdb('1PGB.pdb')
atoms_to_keep = [atom.index for atom in main_pdb.topology.atoms if atom.name == 'CA']
new_pdb = main_pdb.atom_slice(atoms_to_keep)
new_pdb.save('CA_only.pdb')

# Then I try to add a chain and residue, but no results
pdb = PDBFile('CA_only.pdb')
top = topology.Topology
chain=top.addChain(id='A')
residue = top.addResidue(MET, 0)

我可能使用了错误的残留物名称。但我不知道怎么了。有人知道怎么解决这个问题吗？谢谢