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ERROR for assigning angles.

#628Openlaowang-os 创建于 2025-08-06
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laowang-oscommented
Hello, I'm a beginner of Foyer. Forgive my boldness in initiating this corrspondence without prior acquaintance. Here is the situations I met. **Firstly** I ran the following codes for generating a '.pdb' stucture file by mbuild successfully. `import mbuild as mb` `comp_1 = mb.load('[H]c1[nH]c([H])c2c1CCC2', smiles=True)` `comp_1.save('comp_1.pdb')` **Secondly** I ran the following codes for assigning parameters to my '.pdb' file. `import foyer` `import parmed` `mol = parmed.load_file("comp_1.pdb")` `ff = foyer.Forcefield(forcefield_files=['oplsaa.xml'])` `mol_ff = ff.apply(mol)` Then I got the error as following: `FoyerError: Found multiple types for atom 3 (6): ['opls_544', 'opls_141'].` So I used the **'overrides'** command to change the line from `<Type name="opls_544" class="CS" element="C" mass="12.01100" def="[C;X3;r5]([C;%opls_543])" desc="C3 in pyrrole" overrides="opls_142" doi="10.1021/jp981200o"/>` to `<Type name="opls_544" class="CS" element="C" mass="12.01100" def="[C;X3;r5]([C;%opls_543])" desc="C3 in pyrrole" overrides="opls_142,opls_141" doi="10.1021/jp981200o"/>` at the same time I created a new file called 'my_oplsaa.xml'. **Thirdly** I ran the codes `import foyer` `import parmed` `mol = parmed.load_file("comp_1.pdb")` `ff = foyer.Forcefield(forcefield_files=['my_oplsaa.xml'])` `mol_ff = ff.apply(mol)` Then I got the following issue. `Exception: Parameters have not been assigned to all angles. Total system angles: 33, Parameterized angles: 31` **For now I have two questions:** 1. How could I know which two angles didn't parameterized? 2. Once I know the exact angles how could I add the information or modify the '.xml' file and where is the references? **Additionally**, There is also other questions about the Foyer website. In the subsection 'Validation of force field files' of reference section, the link '[XML schema definition](https://foyer.mosdef.org/en/stable/foyer/forcefields/ff.xsd)' and '[syntax](https://foyer.mosdef.org/en/stable/reference/smarts.html)' are invalid nowadays. **I appreciate your time for these issues and regret any disruptiopn my massage may cause.**
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