DNA Backbone Parametrization and rtp File

User discussions
1

Hello,
I am currently working on mutating the backbone of DNA (phosphate) and have a question regarding the parametrization with CGenFF.

Is it necessary to add caps, similar to what is required in the AMBER force field? For example, in AMBER, we typically add caps and create dimethylphosphate before using the Resb server. Is this step also relevant when using CGenFF?

If I add dimethylphosphate, can I remove the dimethyl group in the RTP file?

Furthermore, I downloaded the CHARMM36 files, but I cannot find the specbond.dat and residuetypes.dat files in the directory.

Thank you for your time and assistance.

2

Backbone parametrization is done with dimethylphosphate to start, with charges of the methyl groups becoming those of the corresonding C5’ and C3’ groups. We also use T3PS as a model compound (two furanose rings linked by phosphate to parametrize all relevant dihedrals).