求助cif文件用Multiwfn转换成pdb格式后原子数少了

hanlu · 发表于 Post on 2023-9-21 16:04:47

将MS扩胞后的cif文件在Multiwfn转换成pdb格式，发现转换后pdb格式的文件原子少了39个，尝试很多次，还是少39个原子，求助各位大佬的帮助！！cif文件和Pdb文件在文件包里面，还有MS生成的mol2文件。

0325-ddd · 发表于 Post on 2024-2-3 18:08:43

乐平发表于 2024-2-3 16:48
用 Multiwfn 导入文件后会看到

好的非常感谢，我用gview转化的文件，跑的时候报错，我再试一下您的方法

乐平 · 发表于 Post on 2024-2-3 16:48:56

0325-ddd 发表于 2024-2-3 15:26
您好，想请教一下怎么转化文件呢？

用 Multiwfn 导入文件后会看到

"q": Exit program gracefully "r": Load a new file
************ Main function menu ************
0 Show molecular structure and view orbitals
1 Output all properties at a point 2 Topology analysis
3 Output and plot specific property in a line
4 Output and plot specific property in a plane
5 Output and plot specific property within a spatial region (calc. grid data)
6 Check & modify wavefunction
7 Population analysis and calculation of atomic charges
8 Orbital composition analysis 9 Bond order analysis
10 Plot total DOS, partial DOS, OPDOS, local DOS and photoelectron spectrum
11 Plot IR/Raman/UV-Vis/ECD/VCD/ROA/NMR spectrum
12 Quantitative analysis of molecular surface
13 Process grid data (No grid data is presented currently)
14 Adaptive natural density partitioning (AdNDP) analysis
15 Fuzzy atomic space analysis
16 Charge decomposition analysis (CDA) and plot orbital interaction diagram
17 Basin analysis 18 Electron excitation analysis
19 Orbital localization analysis 20 Visual study of weak interaction
21 Energy decomposition analysis 22 Conceptual DFT (CDFT) analysis
23 ETS-NOCV analysis 24 (Hyper)polarizability analysis
25 Electron delocalization and aromaticity analyses
100 Other functions (Part 1) 200 Other functions (Part 2)
300 Other functions (Part 3)

复制代码

输入 100 后会看到

============ Other functions (Part 1) ============
0 Return
1 Draw scatter graph between two functions and generate their cube files
2 Export various files (mwfn/pdb/xyz/wfn/wfx/molden/fch/47/mkl...) or generate input file of quantum chemistry programs 3 Calculate molecular van der Waals Volume
4 Integrate a function in whole space
5 Show overlap integral between alpha and beta orbitals
6 Monitor SCF convergence process of Gaussian
8 Generate Gaussian input file with initial guess from fragment wavefunctions
9 Evaluate interatomic connectivity and atomic coordination number
11 Calculate overlap and centroid distance between two orbitals
12 Biorthogonalization between alpha and beta orbitals
13 Calculate HOMA and Bird aromaticity index
14 Calculate LOLIPOP (LOL Integrated Pi Over Plane)
15 Calculate intermolecular orbital overlap
17 Generate Fock/KS matrix based on orbital energies and coefficients
18 Yoshizawa's electron transport route analysis
19 Generate new wavefunction by combining fragment wavefunctions
20 Calculate Hellmann-Feynman forces
21 Calculate properties based on geometry information for specific atoms
22 Detect pi orbitals, set occupation numbers and calculate pi composition
23 Fit function distribution to atomic value
24 Obtain NICS_ZZ value for non-planar or tilted system

复制代码

输入 2 后会看到

0 Return
Export system to various formats of files:
1 Output current structure to .pdb file
2 Output current structure to .xyz file
3 Output current structure and atomic charges to .chg file
4 Output current wavefunction as .wfx file
5 Output current wavefunction as .wfn file
6 Output current wavefunction as Molden input file (.molden)
7 Output current wavefunction as .fch file
8 Output current wavefunction as .47 file
9 Output current wavefunction as old Molekel input file (.mkl)
31 Output current structure to .cml file
32 Output current wavefunction as .mwfn file
Generate input file of quantum chemistry codes:
10 Gaussian (with/without initial guess of wavefunction)
11 GAMESS-US (with/without initial guess of wavefunction)
12 ORCA 13 NWChem 14 MOPAC
15 PSI4 16 MRCC 17 CFOUR
18 Molpro 19 Dalton 20 Molcas
21 Q-Chem
25 CP2K 26 Quantum ESPRESSO 27 VASP (POSCAR)

复制代码

然后，你想转换（或者产生）什么格式的文件，就输入对应的编号

0325-ddd · 发表于 Post on 2024-2-3 15:26:52

hanlu 发表于 2023-9-22 09:08
好的，谢谢社长

您好，想请教一下怎么转化文件呢？

hanlu · 发表于 Post on 2023-9-22 09:08:34

好的，谢谢社长

sobereva · 发表于 Post on 2023-9-21 22:28:51

hanlu 发表于 2023-9-21 20:46
不是，MS里面保存的原子数是30727，也就是后面的39个金属原子没了

那是M$自己的事，跟Multiwfn没关系。cif文件里自己用文本编辑器打开就知道本来就只有30688个，VESTA载入cif后同样也是30688个

tsgyls · 发表于 Post on 2023-9-21 22:27:41

hanlu 发表于 2023-9-21 22:00
还有这种情况，谢谢，会不会有些金属原子的坐标是重复的，所以原子数目就多了，

这个我不懂了，应该不会是坐标重复的问题

sobereva · 发表于 Post on 2023-9-21 22:25:51

如置顶的新社员必读贴、论坛首页的公告栏、版头的红色大字非常明确所示，求助帖必须在帖子标题明确体现出此帖内容是求助或提问，并清楚、准确反映出帖子具体内容，避免有任何歧义和含糊性，仔细看http://bbs.keinsci.com/thread-9348-1-1.html。我已把你的不恰当标题 “格式文件的转换” 改了，以后务必注意

hanlu · 发表于 Post on 2023-9-21 22:00:33

tsgyls 发表于 2023-9-21 21:31
我用openbabel转换的时候也少了最后的金属原子，可能是格式转换的通病？
或者你可以手动添加

还有这种情况，谢谢，会不会有些金属原子的坐标是重复的，所以原子数目就多了，

tsgyls · 发表于 Post on 2023-9-21 21:31:21

我用openbabel转换的时候也少了最后的金属原子，可能是格式转换的通病？
或者你可以手动添加

hanlu · 发表于 Post on 2023-9-21 20:46:16

pal 发表于 2023-9-21 20:14
不都是30688个么

不是，MS里面保存的原子数是30727，也就是后面的39个金属原子没了

pal · 发表于 Post on 2023-9-21 20:14:07

不都是30688个么

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[Multiwfn使用咨询] 求助cif文件用Multiwfn转换成pdb格式后原子数少了