Hi all,
Thanks for taking the time to help me. I have generated a charged oligomer chain using acepype, as it is the only software I have been able to find to automatically parametrize using the OPLS-AA force field. However, the output file indicates that there are atoms that it could not define. I have attached the files for further clarity. Would it be enough to define these groups by hand, assigning them to the functional groups that suit them best in the topology file with this force field?
When generating topology files with acpype (which uses Antechamber and GAFF primarily), encountering undefined atoms or residues when using the OPLS-AA force field is relatively common, especially if acpype cannot match certain groups with the correct parameters in its database. If your output file has unidentified atoms, manually assigning them in the topology file can work, especially if you have a clear understanding of the groups involved and the functional groups they resemble.
Here are some steps and best practices:
Alternatively, tools like LigParGen or ParamChem might be able to assist with parameterization using OPLS-AA, though these tools may have limitations on specific oligomer types.
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