Hello everyone,
I am trying to simulate a system with a protein, both in the wild-type and mutant form, containing two Cu2+ and two Zn2+ ions. These are the parameters I load using leap
source leaprc.protein.ff19SB
source leaprc.water.opc
loadAmberParams frcmod.ionslm_1264_opc
My issue is that, after the heating, relaxation, and minimization steps finish and the production starts, the two copper ions leave the complexes with the protein, while the two zinc ions don’t. This happens with both 1264 and 126 parameters.
I would like to avoid using the bonded model, because I am afraid I would introduce a bias, especially in the mutated proteins, where the loss of copper might be a significant result.
I don’t think there is an issue with my protein per se, because during simulations of the wild-type complex performed with another software, none of the ions detached. So, I hypothesize that there might be an issue with my parametrization.
What could I attempt?
Thank you in advance for your suggestions.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 28 2024 - 05:30:02 PST
