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Dear Developers,
I would like to build a polymer (Like PIM-1) with two heads and two tails. I can find examples with single head and tail and procedures to assign them. However, I am finding it difficult to define two heads in the code. Could you please provide some examples?
If you can please edit the following code to assign two heads that would be great.
def monomer():
s = system.read_mol('My.mol'))
m = s.molecules[1]
f = forcefield.Gaff2()
for b in s.bonds:
if b.a.bonds.count == 3 and b.b.bonds.count == 3:
b.order = 4
s.apply_forcefield(f)
c1 = s.particles[1] #head 1
c2 = s.particles[2] #head 2
c5 = s.particles[5] #tail 1
c5 = s.particles[6] #tail 2
for b in c1.bonds:
if b.a.elem == 'H' or b.b.elem == 'H':
pb = b.a if b.b is c1 else b.b
s.particles.remove(pb.tag, update=False)
break
for b in c5.bonds:
if b.a.elem == 'H' or b.b.elem == 'H':
pb = b.a if b.b is c1 else b.b
s.particles.remove(pb.tag, update=False)
break
s.remove_spare_bonding()
c1.linker = 'head'
#c2.linker= 'head'
c5.linker = 'tail'
#c6.linker= 'tail'
lmps.quick_min(s, min_style='fire')
s.add_particle_bonding()
return s
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