I hope you all are doing well! I am not sure why I start to see little charge in .top file after using antechamber with GAFF force field to convert into Gromacs format? Can anyone please advise how I should get rid off of the charge in .top file which is q=0.005?
Thanks in advance!
Charge information are in the topology file (topol.top) and topology files (topol.top) do not change after you have generated them. Could you try to reformulate your question?
Thanks for your response! I meant that I am using ParmEd to generate .top and .gro file to be used in Gromacs format. However, my topology file inheritently gets qtot=0.005 when it’s generate by ParmEd.