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标题: gromacs模拟麦芽糖不能生成gro和top文件？ [打印本页]

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Author: baimengyao 时间: 2025-4-1 09:29
标题: gromacs模拟麦芽糖不能生成gro和top文件？
老师好，我用CHARMM-GUI生成的麦芽糖pdb文件，
但在调用gmx pdb2gmx -ff charmm36-jul2022 -f maltose.pdb -o maltose3.gro -water tip3p -p  maltose.top -i maltose.itp命令时候，
提示 “Fatal error:Residue 2 named AGLC of a molecule in the input file was mapped
to an entry in the topology database, but the atom O1 used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.“
但是在单独模拟葡萄糖的时候就能成功，我找了carb.rtp里面也没有包含麦芽糖的残基
输入文件如下：

REMARK  GENERATE GLYCAN
REMARK DATE:    3/29/25    5:36:26    CREATED BY USER: charmm-gui
ATOM    1  C1  AGLC 1    -0.733 0.818 1.091  1.00  0.00    CARB
ATOM    2  H1  AGLC 1    -1.822 0.741 0.871  1.00  0.00    CARB
ATOM    3  O1  AGLC 1    -0.603 0.702 2.488  1.00  0.00    CARB
ATOM    4  HO1 AGLC 1    -1.312 1.193 2.909  1.00  0.00    CARB
ATOM    5  C5  AGLC 1    1.132 2.260 0.652  1.00  0.00    CARB
ATOM    6  H5  AGLC 1    1.402 2.206 1.733  1.00  0.00    CARB
ATOM    7  O5  AGLC 1    -0.286 2.051 0.512  1.00  0.00    CARB
ATOM    8  C2  AGLC 1    -0.022  -0.322 0.386  1.00  0.00    CARB
ATOM    9  H2  AGLC 1    -0.297  -0.272  -0.695  1.00  0.00    CARB
ATOM    10  O2  AGLC 1    -0.472  -1.591 0.845  1.00  0.00    CARB
ATOM    11  HO2 AGLC 1    -0.272  -1.672 1.781  1.00  0.00    CARB
ATOM    12  C3  AGLC 1    1.480  -0.173 0.492  1.00  0.00    CARB
ATOM    13  H3  AGLC 1    1.776  -0.189 1.567  1.00  0.00    CARB
ATOM    14  O3  AGLC 1    2.164  -1.252  -0.124  1.00  0.00    CARB
ATOM    15  HO3 AGLC 1    2.596  -1.775 0.554  1.00  0.00    CARB
ATOM    16  C4  AGLC 1    1.881 1.162  -0.095  1.00  0.00    CARB
ATOM    17  H4  AGLC 1    1.582 1.212  -1.169  1.00  0.00    CARB
ATOM    18  O4  AGLC 1    3.293 1.376 0.016  1.00  0.00    CARB
ATOM    19  C6  AGLC 1    1.448 3.655 0.164  1.00  0.00    CARB
ATOM    20  H61 AGLC 1    2.508 3.893 0.381  1.00  0.00    CARB
ATOM    21  H62 AGLC 1    1.280 3.737  -0.932  1.00  0.00    CARB
ATOM    22  O6  AGLC 1    0.656 4.639 0.820  1.00  0.00    CARB
ATOM    23  HO6 AGLC 1    -0.235 4.612 0.464  1.00  0.00    CARB
ATOM    24  C1  AGLC 2    4.029 1.053  -1.146  1.00  0.00    CARB
ATOM    25  H1  AGLC 2    3.558 0.192  -1.671  1.00  0.00    CARB
ATOM    26  C5  AGLC 2    4.794 3.293  -1.606  1.00  0.00    CARB
ATOM    27  H5  AGLC 2    4.282 3.660  -0.689  1.00  0.00    CARB
ATOM    28  O5  AGLC 2    4.107 2.128  -2.095  1.00  0.00    CARB
ATOM    29  C2  AGLC 2    5.439 0.666  -0.758  1.00  0.00    CARB
ATOM    30  H2  AGLC 2    5.963 0.305  -1.676  1.00  0.00    CARB
ATOM    31  O2  AGLC 2    5.417  -0.426 0.149  1.00  0.00    CARB
ATOM    32  HO2 AGLC 2    4.969  -0.153 0.953  1.00  0.00    CARB
ATOM    33  C3  AGLC 2    6.207 1.840  -0.199  1.00  0.00    CARB
ATOM    34  H3  AGLC 2    5.686 2.214 0.715  1.00  0.00    CARB
ATOM    35  O3  AGLC 2    7.522 1.474 0.196  1.00  0.00    CARB
ATOM    36  HO3 AGLC 2    7.998 1.145  -0.570  1.00  0.00    CARB
ATOM    37  C4  AGLC 2    6.224 2.933  -1.238  1.00  0.00    CARB
ATOM    38  H4  AGLC 2    6.748 2.572  -2.154  1.00  0.00    CARB
ATOM    39  O4  AGLC 2    6.918 4.081  -0.780  1.00  0.00    CARB
ATOM    40  HO4 AGLC 2    7.749 4.154  -1.255  1.00  0.00    CARB
ATOM    41  C6  AGLC 2    4.694 4.359  -2.676  1.00  0.00    CARB
ATOM    42  H61 AGLC 2    5.203 5.289  -2.344  1.00  0.00    CARB
ATOM    43  H62 AGLC 2    5.178 4.013  -3.615  1.00  0.00    CARB
ATOM    44  O6  AGLC 2    3.338 4.689  -2.958  1.00  0.00    CARB
ATOM    45  HO6 AGLC 2    2.944 3.979  -3.470  1.00  0.00    CARB
TER    46    AGLC    2
请问老师，这种问题怎么解决？

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