Here is what I'm trying to do: to solvate a peptide in water and ions that would mimic a PBS solution.
To do this I tried uploading my peptide into the Solution Builder, adding the following ions:
NaCl 0.14 M
KCl 0.003 M
Na2HPO4 0.008 M
KH2PO4 0.002 M
And I increased the waterbox size until I had at least 1 H2PO4 ion in the solution with ion calculation.
I need to run a GROMACS simulation using a AMBER 19SBff, but when I click this at the end of the CHARMM-GUI process it warns me that it cant find the HPO4 in the force field:
"Error: Could not find residue (HPO4) in the force field"
I tried this with varying lengths of peptide, from 11 to 37 aa.
I tried Monte-Carlo and Distance placing methods.
I tried changing which ion is neutralizing.
I tried increasing the concentrations to 0.15M for every component.
I tried using PO4 ions as well - it doesnt work regardless.
I even tried to build the ff for the ions through Ligand Modeler and using Multicomponent Assembler to make the solution and it still gave the same response.
What am I missing? Someone please help.
PS - before someone tells me AMBER cant simulate this molecule, I had made one such AMBER simulation once by accident and not once since then. But because I was pushing out 20 simulations a day I missed what I did differently.
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