[AMBER] Help parameterizing iron citrate

From: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>
Date: Fri, 17 Dec 2021 02:29:00 -0500

Dear Amber Community,

I’m trying to parameterize a trimeric iron(III) citrate (3:3 ratio of iron to citrate) complex that also has one of the coordination sites to an iron occupied by a water molecule. I have a few questions regarding the procedure.

1) For the citrate ligand, I successfully followed the Sustiva tutorial <https://ambermd.org/tutorials/basic/tutorial4b/index.php>. In the generated frcmod, I have two warnings: "Calculated with empirical approach for c-c3-o” for an angle and "Using general improper torsional angle X- o- c- o, penalty score= 3.0)” for an improper torsion. Should I worry about fixing these parameters now, or later in the context of the chelated Fe? Either way, how would I improve these bonded parameters?

2) My plan was to next use MCPB for the trimeric iron citrate complex. But, how do I include the water ligand? Do I need to generate a mol2 file of the water to pass to naa_mol2files in the input file, along with the mol2 for citrate? If so, how would you recommend generating that water mol2?


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Received on Thu Dec 16 2021 - 23:30:02 PST
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