将蛋白质pdb转化为orca输入文件时元素识别出错

wuzhiyi · 发表于 Post on 2020-2-23 04:42:04

我想将一个蛋白质的pdb文件转化为orca的输入文件，却发现histindine的NE2被识别为了Ne元素。
希望Multiwfn可以支持pdb标准氨基酸命名模式
在https://cdn.rcsb.org/wwpdb/docs/documentation/file-format/PDB_format_1992.pdf 第27页有明确的写明每个氨基酸里的原子应该怎么命名。

我的输入文件

REMARK 4 COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006
REMARK 888
REMARK 888 WRITTEN BY MAESTRO (A PRODUCT OF SCHRODINGER, LLC)
TITLE crystal
MODEL 1
ATOM 71 N HIS B 5 26.806 37.427 79.456 1.00 62.10 N
ANISOU 71 N HIS B 5 5469 8248 9880 -589 813 244
ATOM 72 CA HIS B 5 28.223 37.642 79.135 1.00 59.01 C
ANISOU 72 CA HIS B 5 5266 7756 9397 -561 804 194
ATOM 73 C HIS B 5 28.567 36.819 77.908 1.00 59.69 C
ANISOU 73 C HIS B 5 5381 7890 9406 -672 682 117
ATOM 74 O HIS B 5 28.839 35.623 78.013 1.00 58.83 O
ANISOU 74 O HIS B 5 5322 7726 9304 -795 677 30
ATOM 75 CB HIS B 5 29.133 37.309 80.333 1.00 58.59 C
ANISOU 75 CB HIS B 5 5361 7547 9353 -563 914 149
ATOM 76 CG HIS B 5 28.877 38.158 81.539 1.00 61.21 C
ANISOU 76 CG HIS B 5 5691 7835 9731 -448 1032 204
ATOM 77 ND1 HIS B 5 28.823 39.543 81.455 1.00 62.58 N
ANISOU 77 ND1 HIS B 5 5858 8012 9906 -306 1049 263
ATOM 78 CD2 HIS B 5 28.665 37.792 82.824 1.00 62.52 C
ANISOU 78 CD2 HIS B 5 5870 7950 9934 -451 1140 205
ATOM 79 CE1 HIS B 5 28.587 39.967 82.684 1.00 61.88 C
ANISOU 79 CE1 HIS B 5 5783 7872 9855 -229 1165 278
ATOM 80 NE2 HIS B 5 28.475 38.951 83.541 1.00 62.18 N1+
ANISOU 80 NE2 HIS B 5 5833 7888 9905 -309 1224 248
ATOM 81 H HIS B 5 26.583 36.550 79.905 1.00 0.00 H
ATOM 82 HA HIS B 5 28.359 38.695 78.887 1.00 0.00 H
ATOM 83 HB3 HIS B 5 30.176 37.411 80.034 1.00 0.00 H
ATOM 84 HB2 HIS B 5 29.012 36.259 80.598 1.00 0.00 H
ATOM 86 HD2 HIS B 5 28.671 36.747 83.096 1.00 0.00 H
ATOM 87 HE1 HIS B 5 28.509 41.025 82.884 1.00 0.00 H
ATOM 88 HE2 HIS B 5 28.291 38.907 84.533 1.00 0.00 H
ATOM 89 N ASP B 6 28.481 37.456 76.734 1.00 54.69 N
ANISOU 89 N ASP B 6 4715 7367 8700 -623 587 153
ATOM 90 CA ASP B 6 28.686 36.822 75.433 1.00 53.85 C
ANISOU 90 CA ASP B 6 4629 7343 8490 -709 463 82
ATOM 91 H ASP B 6 28.261 38.442 76.709 1.00 0.00 H
ATOM 92 HA1 ASP B 6 28.558 37.562 74.643 1.00 0.00 H
ATOM 93 HA2 ASP B 6 29.694 36.409 75.384 1.00 0.00 H
ATOM 94 HA3 ASP B 6 27.959 36.021 75.300 1.00 0.00 H
ENDMDL
END

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得到的输出文件

! B97-3c noautostart miniprint nopop
%maxcore 1000
%pal nprocs 4 end
* xyz 0 1
N 26.80600000 37.42700000 79.45600000
C 28.22300000 37.64200000 79.13500000
C 28.56700000 36.81900000 77.90800000
O 28.83900000 35.62300000 78.01300000
C 29.13300000 37.30900000 80.33300000
C 28.87700000 38.15800000 81.53900000
N 28.82300000 39.54300000 81.45500000
C 28.66500000 37.79200000 82.82400000
C 28.58700000 39.96700000 82.68400000
Ne 28.47500000 38.95100000 83.54100000
H 26.58300000 36.55000000 79.90500000
H 28.35900000 38.69500000 78.88700000
H 30.17600000 37.41100000 80.03400000
H 29.01200000 36.25900000 80.59800000
H 28.67100000 36.74700000 83.09600000
H 28.50900000 41.02500000 82.88400000
H 28.29100000 38.90700000 84.53300000
N 28.48100000 37.45600000 76.73400000
C 28.68600000 36.82200000 75.43300000
H 28.26100000 38.44200000 76.70900000
H 28.55800000 37.56200000 74.64300000
H 29.69400000 36.40900000 75.38400000
H 27.95900000 36.02100000 75.30000000
*

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可见命名为NE2且元素一栏标明N的原子被转换为了Ne元素

sobereva · 发表于 Post on 2020-2-23 18:59:26

Multiwfn不是专门面向生物分子的，所以这个不打算实现
这种问题最好的解决办法就是让pdb严格符合标准的规范，即pdb文件的元素那一列直接定义清楚元素。目前的Multiwfn是优先从那一列判断元素的，没有的时候才根据原子名去猜。

wuzhiyi · 发表于 Post on 2020-2-23 19:31:19

sobereva 发表于 2020-2-23 18:59
Multiwfn不是专门面向生物分子的，所以这个不打算实现
这种问题最好的解决办法就是让pdb严格符合标准的规 ...

谢谢sob老师的解答，可是源文件中有标明元素。
ATOM 80 NE2 HIS B 5 28.475 38.951 83.541 1.00 62.18 N1+
可见元素那一行写明了N
可转化为orca输入文件之后仍识别为了Ne
Ne 28.47500000 38.95100000 83.54100000

sobereva · 发表于 Post on 2020-2-23 19:38:28

wuzhiyi 发表于 2020-2-23 19:31
谢谢sob老师的解答，可是源文件中有标明元素。
ATOM 80 NE2 HIS B 5 28.475 38.951 83.54 ...

应当写成N。把1+去掉。

wuzhiyi · 发表于 Post on 2020-2-23 19:52:16

sobereva 发表于 2020-2-23 19:38
应当写成N。把1+去掉。

谢谢sob老师

zsu007 · 发表于 Post on 2020-2-24 19:32:50

楼主，是否可以先把pdb文件转成为sdf文件，再打开sdf文件即可。

ene · 发表于 Post on 2020-2-24 21:28:52

建议先用pymol把pdb转换成xyz格式，然后再导入Multiwfn。VMD有时候可能会有坑，有的元素名不正确。

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