Gromacs用x2top生成硅铝分子筛的itp时报错

Mingyu

求助各位大佬，我的硅铝分子筛共有硅铝氧氢四种元素，规律排列。
用的Amber力场，在ffnonbonded里添加了这四个元素的立场参数。


以下是我的n2t文件：


Si SI  2.1  28.0855 4 O  0.162  O  0.162 O 0.162 O 0.162
Si SI  2.1  28.0855 3 O  0.162  O  0.162 O 0.162
Si SI  2.1  28.0855 2 O  0.162  O  0.162
Si SI  2.1  28.0855 1 O  0.162

Al AL  1.6  26.9815 4 O  0.195  O  0.170 O 0.170 O 0.170

H  HH  0.5  1.0000  1 O  0.099

O  O1 -1.05 15.9994 3 H  0.099  Al 0.195 Si 0.162
O  O1 -1.05 15.9994 2 Si 0.162  Si 0.162
O  O1 -1.05 15.9994 2 Si 0.162  Al 0.170
O  O1 -1.05 15.9994 1 Si 0.162


我的命令：gmx x2top -f SiO.pdb -o top.top -ff select -nopbc -name SIO -kb 400000 -kt 800 -kp 200
选择力场后报错如下：
Can not find forcefield for atom O21-216 with 1 bonds
Can not find forcefield for atom 5H29-289 with 0 bonds
Can not find forcefield for atom 2H30-290 with 0 bonds
Can not find forcefield for atom O21-506 with 1 bonds
Can not find forcefield for atom 5H29-579 with 0 bonds
Can not find forcefield for atom 2H30-580 with 0 bonds
Can not find forcefield for atom O21-796 with 1 bonds
Can not find forcefield for atom 5H29-869 with 0 bonds
Can not find forcefield for atom 2H30-870 with 0 bonds
Can not find forcefield for atom O21-1086 with 1 bonds
Can not find forcefield for atom 5H29-1159 with 0 bonds
Can not find forcefield for atom 2H30-1160 with 0 bonds
Can not find forcefield for atom 5H29-1449 with 0 bonds
Can not find forcefield for atom 2H30-1450 with 0 bonds
Can not find forcefield for atom 5H29-1739 with 0 bonds
Can not find forcefield for atom 2H30-1740 with 0 bonds
Can not find forcefield for atom 5H29-2029 with 0 bonds
Can not find forcefield for atom 2H30-2030 with 0 bonds
Can not find forcefield for atom 5H29-2319 with 0 bonds
Can not find forcefield for atom 2H30-2320 with 0 bonds
Can not find forcefield for atom 5H29-2609 with 0 bonds
Can not find forcefield for atom 2H30-2610 with 0 bonds
Can not find forcefield for atom 5H29-2899 with 0 bonds
Can not find forcefield for atom 2H30-2900 with 0 bonds
Can not find forcefield for atom 5H29-3189 with 0 bonds
Can not find forcefield for atom 2H30-3190 with 0 bonds
Can not find forcefield for atom 5H29-3479 with 0 bonds
Can not find forcefield for atom 2H30-3480 with 0 bonds
Can not find forcefield for atom O25-3734 with 1 bonds
Can not find forcefield for atom 5H29-3769 with 0 bonds
Can not find forcefield for atom 2H30-3770 with 0 bonds
Can not find forcefield for atom O25-4024 with 1 bonds
Can not find forcefield for atom 5H29-4059 with 0 bonds
Can not find forcefield for atom 2H30-4060 with 0 bonds
Can not find forcefield for atom O25-4314 with 1 bonds
Can not find forcefield for atom 5H29-4349 with 0 bonds
Can not find forcefield for atom 2H30-4350 with 0 bonds
Can not find forcefield for atom O25-4604 with 1 bonds
Can not find forcefield for atom 5H29-4639 with 0 bonds
Can not find forcefield for atom 2H30-4640 with 0 bonds

-------------------------------------------------------
Program:     gmx x2top, version 2022
Source file: src/gromacs/gmxpreprocess/x2top.cpp (line 180)

Fatal error:
Could only find a forcefield type for 4600 out of 4640 atoms


有四十个原子一直显示找不到力场类型。请各位大佬帮忙检查一下，感谢！！！@sobereva

sobereva

参考sobtop主页http://sobereva.com/soft/Sobtop里的二氧化硅的例子，举一反三

Mingyu

sobereva 发表于 2024-11-10 18:38
参考sobtop主页http://sobereva.com/soft/Sobtop里的二氧化硅的例子，举一反三

谢谢sob老师，还是sobtop好用！