Charge issue when Antechamber generated .top file with GAFF forcefield get used in Gromacs

User discussions
1

Hi Everyone,

Can anyone please tell me how to resolve the inherited charge issue between Gromacs and Antechamber file?

“Note that very small differences between charges in the GAFF and GROMACS files may occur because the charges as generated by the Antechamber suite did not add up to zero, whereas this is needed in GROMACS.”

Thanks in advance!

2

You can approximate it to higher decimal point or modify by slight adjustment for the calculated charges to become zero

3

Thanks for your response!
This process can take a while to do it manually on excel especially when there are >50 atoms in a molecule. I am wondering whether I can somehow automate this process?

4

I don’t know any different method

5

Just to clarify. You also manually do this process in excel?

6

Yes, especially when transferring charges obtained from QM to itp file