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Hello,
I am trying to add an alkyl chain to the backbone of DNA. To obtain the parameters, I used CHARMM-GUI. However, I encountered an issue:
Initially, I added only the backbone with a methyl group (as shown in the attached image) to CHARMM-GUI. After obtaining the parameters, I deleted the methyl group along with its attached oxygen and hydrogen. When I added this modified structure as a new residue in GROMACS, the total charge was not an integer. Specifically, I expected a total charge of -19, but I obtained -19.738 e instead.(attched file)
I have a question about how to properly obtain parameters for the backbone. I tried uploading thymine with the attached alkyl chain, but the resulting charge penalty was high. Additionally, it is not clear to me how to cap the backbone to obtain parameters correctly from CHARMM-GUI.
Could someone please help me understand why this is happening and guide me on how to resolve this issue?
Thank you!
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