[已解决]pdb2gmx建纤维素拓扑.gro中最后一个糖环氧原子坐标错误

zdworld · 发表于 Post on 2023-4-26 16:30:06

本帖最后由 zdworld 于 2023-4-27 14:28 编辑

已解决，不要手动调整原子顺序，写个脚本批量改一下就行了。
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gromacs版本：2020.6-MODIFIED
力场：gromose53a6carbo
cellulose builder产生的纤维素pdb会把糖苷键上的O认为是O4，53a6carbo力场认为是O1，手动修改后直接gmx pdb2gmx -f cellulose.pdb -o cellulose.gro -p cellulose.top -ignh前面的糖环都没有问题，但是最后一个糖环O1和O4位置刚好反了，加氢之后变成这样：

128号氧和142号氧位置反了，但是产生的拓扑没问题，不知道这种情况是为什么。
gromacs输出为：
WARNING: there were 1 atoms with zero occupancy and 0 atoms with
      occupancy unequal to one (out of 111 atoms). Check your pdb file.
...
Processing chain 1 (111 atoms, 10 residues)
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
8 out of 8 lines of specbond.dat converted successfully
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 10 residues with 143 atoms
Making bonds...
Warning: Long Bond (127-128 = 0.649585 nm)
Warning: Long Bond (128-129 = 0.412383 nm)
Warning: Long Bond (141-142 = 0.410297 nm)
Number of bonds was 152, now 152
Generating angles, dihedrals and pairs...
Before cleaning: 310 pairs
Before cleaning: 358 dihedrals
Making cmap torsions...
There are  256 dihedrals, 50 impropers,  211 angles
         280 pairs,    152 bonds and    0 virtual sites
Total mass 1639.445 a.m.u.
Total charge -0.000 e
Writing topology
Writing coordinate file...

Back Off! I just backed up cellulose.gro to ./#cellulose.gro.1#
            --------- PLEASE NOTE ------------
You have successfully generated a topology from: crystal.pdb.
The Gromos53a6carbo force field is used.
            --------- ETON ESAELP ------------

pdb文件，gro文件和top文件：

cellulose.pdb (16.44 KB, 下载次数 Times of downloads: 13)

cellulose.gro (6.51 KB, 下载次数 Times of downloads: 3)

cellulose.top (41.49 KB, 下载次数 Times of downloads: 0)

xuxuxu · 发表于 Post on 2023-7-2 22:19:06

老哥，我也遇到这个问题了。不知道怎么修改，求赐教

zdworld · 发表于 Post on 2023-8-2 11:13:10

xuxuxu 发表于 2023-7-2 22:19
老哥，我也遇到这个问题了。不知道怎么修改，求赐教

这个跟力场有关，中间的氧原子归属不同来源的结构会有不同，需要自己改改。

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[GROMACS] [已解决]pdb2gmx建纤维素拓扑.gro中最后一个糖环氧原子坐标错误