[gmx-users] Re: polymer duplicate atoms

[cqgzc]

I have successfully construct the polymer chain of length 1 using the OPLS
force field. The rtp file as follow:

; F2311 - this is an internal residue
[ Fre ]
  [ atoms ]
    C1    opls_135           -0.568    1
    H11   opls_140            0.274    1
    H12   opls_140            0.273    1
    C2    opls_962            0.373    2
    F21   opls_965           -0.165    2
    F22   opls_965           -0.159    2
    C3    opls_962            0.182    3
    F31   opls_965           -0.133    3
    F32   opls_965           -0.144    3
    C4    opls_963            0.142    4
    F4    opls_965           -0.142    4
    Cl4   opls_151            0.066    4
  [ bonds ]
    C1    -C4
    C1    H11
    C1    H12
    C1    C2
    C2    F21
    C2    F22
    C2    +C3
    C3    F31
    C3    F32
    C3    C4
    C4    F4
    C4    Cl4
    C4    +C1

; Terminal f2311 residue ("beginning" of chain)
; designation arbitrary, C1 is -CH3
[ Fbg ]
  [ atoms ]
    C1    opls_135           -0.565     1
    H11   opls_140            0.198     1
    H12   opls_140            0.208     1
    H13   opls_140            0.209     1
  [ bonds ]
    C1    H11
    C1    H12
    C1    H13
; Terminal f2311 residue ("end" of chain)
; designation arbitrary, C1 is -CH3
[ Fen ]
  [ atoms ]
    C1    opls_135           -0.705    1
    H11   opls_140            0.248    1
    H12   opls_140            0.246    1
    H13   opls_140            0.245    1
  [ bonds ]
    C1    H11
    C1    H12
    C1    H13




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