Resolving Charge Imbalance for CHARMM DNA Backbone Parameterization in GROMACS

User discussions
1

@awacha

Hello,

I am currently working on parameterizing the DNA backbone and have explored the CHARMM-GUI documentation here. Following the instructions, I added a methyl group to cap the backbone and hydrogens to the O3’ and O5’ groups, which allowed me to obtain charge parameterization using CHARMM-GUI.

However, when I remove the methyl group from phosphorus and the hydrogen and oxygen from the nucleotide, I encounter an issue with the total charge. Specifically:

After removing the methyl group, the total remaining charge is -0.4740000000000002.
After removing the OH group from the nucleotide, the total remaining charge is 0.45999999999999996.
When I attempt to define these in GROMACS as a new residue in the .rtp file, the total charge does not sum to zero, which is problematic.

Could you please provide guidance on how to address this issue or correct the charges?I would appreciate it if you could fix my method if it is wrong.

Thank you in advance for your assistance!
I have attached the itp file.
combine_itp.txt (5.4 KB)

Best regards,
Fatemeh,

2

This is an issue for CHARMM-GUI, not GROMACS. GROMACS simply sums up the charges it is given and then produces a warning.

3

thank you for your reply.
Best regards,
Fatemeh,