标题: 构建非标准残基残基名映射报错 [打印本页] 作者Author: 2535882172 时间: 2023-11-26 23:20 标题: 构建非标准残基残基名映射报错 在进行非标准残基模拟时，设定179为非标准残基MOL，输入gmx pdb2gmx -f pro.pdb -o pro.gro -p pro.top -ignh 对输入结构进行拓扑处理
报错如下：
Fatal error:
Residue 180 named MOL of a molecule in the input file was mapped
to an entry in the topology database, but the atom C used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
然后我检查了pdb文件，确认180号残基没有命名错误
ATOM 30 H30 MOL A 179 84.386 15.296 47.902 0.00 0.00 H
ATOM 31 H31 MOL A 179 84.838 13.645 47.550 0.00 0.00 H
ATOM 32 H32 MOL A 179 91.858 19.577 45.055 0.00 0.00 H
ATOM 33 H33 MOL A 179 91.504 18.088 41.722 0.00 0.00 H
ATOM 34 H34 MOL A 179 85.940 18.121 47.849 0.00 0.00 H
ATOM 35 H35 MOL A 179 82.132 17.547 40.433 0.00 0.00 H
ATOM 36 H36 MOL A 179 82.419 17.094 43.276 0.00 0.00 H
ATOM 37 H37 MOL A 179 83.445 19.442 41.622 0.00 0.00 H
ATOM 38 H38 MOL A 179 84.234 17.901 41.725 0.00 0.00 H
ATOM 39 H39 MOL A 179 84.383 18.139 44.233 0.00 0.00 H
ATOM 40 H40 MOL A 179 83.682 19.730 44.060 0.00 0.00 H
ATOM 41 H41 MOL A 179 85.546 20.484 42.650 0.00 0.00 H
ATOM 42 H42 MOL A 179 86.251 18.909 42.673 0.00 0.00 H
ATOM 43 H43 MOL A 179 86.171 20.917 44.969 0.00 0.00 H
ATOM 44 H44 MOL A 179 87.526 20.168 44.227 0.00 0.00 H
ATOM 45 H45 MOL A 179 85.588 19.016 46.072 0.00 0.00 H
ATOM 2876 N ASN A 180 80.727 18.579 44.358 1.00 98.86 N
ATOM 2877 CA ASN A 180 79.519 19.160 44.954 1.00 98.86 C
ATOM 2878 C ASN A 180 79.707 19.463 46.451 1.00 98.86 C
ATOM 2879 O ASN A 180 80.665 18.991 47.070 1.00 98.86 O
ATOM 2880 CB ASN A 180 78.347 18.191 44.723 1.00 98.86 C
ATOM 2881 CG ASN A 180 78.485 16.933 45.560 1.00 98.86 C
ATOM 2882 ND2 ASN A 180 79.092 15.892 45.039 1.00 98.86 N
ATOM 2883 OD1 ASN A 180 78.112 16.903 46.717 1.00 98.86 O
ATOM 2884 H ASN A 180 81.159 17.823 44.869 1.00 98.86 H
ATOM 2885 HA ASN A 180 79.281 20.102 44.458 1.00 98.86 H
ATOM 2886 HB2 ASN A 180 77.407 18.671 44.999 1.00 98.86 H
ATOM 2887 HB3 ASN A 180 78.286 17.930 43.667 1.00 98.86 H
ATOM 2888 HD21 ASN A 180 79.399 15.901 44.077 1.00 98.86 H
ATOM 2889 HD22 ASN A 180 79.065 15.042 45.585 1.00 98.86 H