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UNL couldn't be found in amino acid xyz. #37

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SangniXun opened this issue Jan 24, 2024 · 0 comments
Open

UNL couldn't be found in amino acid xyz. #37

SangniXun opened this issue Jan 24, 2024 · 0 comments

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@SangniXun
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    pdb1 = open('solute.xyz.pdb').readlines()
    pdb2 = open('solute.xyz.pdb','w')
    for line in pdb1:
        newline = line.replace('UNL','SLU')
        pdb2.write(newline)
    pdb2.close()

amino acid will be recognized by openbabel. There is no UNL in column[18:21]
COMPND (2S)-2-Amino-5-(diaminomethylideneamino)pentanoic acid
AUTHOR GENERATED BY OPEN BABEL 3.1.0
ATOM 1 N ARG A 1 0.859 -2.910 -0.858 1.00 0.00 N
ATOM 2 CA ARG A 1 1.335 -1.538 -1.153 1.00 0.00 C
ATOM 3 C ARG A 1 2.860 -1.566 -1.162 1.00 0.00 C
ATOM 4 OXT ARG A 1 3.625 -1.897 -0.276 1.00 0.00 O
ATOM 5 O ARG A 1 3.429 -1.149 -2.316 1.00 0.00 O
ATOM 6 CB ARG A 1 0.870 -0.461 -0.160 1.00 0.00 C
ATOM 7 HB1 ARG A 1 1.471 0.458 -0.312 1.00 0.00 H
ATOM 8 HB2 ARG A 1 1.077 -0.780 0.883 1.00 0.00 H
ATOM 9 CG ARG A 1 -0.605 -0.131 -0.327 1.00 0.00 C

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