Hello all. I am working on a ligand-dmso system using GROMACS. My system is supposed to be neutral but it is showing that it has an overall charge of 0.022153. I believe this is happening due to parametrization. I tried to add ions to neutralize the system, but it didn't solve the issue. What can be done to make the system neutral. Any suggestions ??
I suggest editing the topology file. You can distribute the -0.022153 to some atoms for example oxygen or hydrogen in the alkyl groups. Alternatively, you can reduce the positive charge of some atoms (maybe sulfurs).
I think Khabib Khumaini is right.
You can't fix this problem via GROMACS, since the charge is supposed to be an integer. The amount you are left with is mostly coming from the topology you built. It seems way too large to be a spurious contribution coming from any round-off error, therefore you must fix it by redistributing the charges in the topology up until you reach an integer value of the charge, which can then be countered by the addition of ions. However, I have no idea about how you should redistribute the charge values. Probably a good way could be that of finding in literature published papers that use molecules similar to yours and start/take ideas from their topology.
Hi,
You can reparameterize the ligand to get new charges. You can do it in AMBER RED server or in CHARMM GUI. Otherwise, there will be artifacts.
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