[AMBER] Li salt parameterisation issue

From: Damiano Spadoni <Damiano.Spadoni.nottingham.ac.uk>
Date: Tue, 28 Dec 2021 15:26:29 +0000

Hi AMBER community,

I hope you're all having a great time.
I am trying to set up MD simulations in AMBER20 of a box cell containing organic solvents and LiTFSI (lithium bis(trifluoromethanesulfonyl)imide) salt.
I made QM optimisation of the molecule in order to retrieve its parameters through RESP charges.
I followed the following tutorial: http://ambermd.org/antechamber/efz.html.
Generate topology file for HIV-1 RT/EFZ - AMBER<http://ambermd.org/antechamber/efz.html>
HIV-1 RT /EFZ Step 1: Extract EFZ.pdb from 1FK9.pdb ; Step 2: Edit EFZ.pdb with sybyl (modify atom types, bond types and add hydrogen atoms) and save out a mol2 file EFZ_sybyl.mol2 (Take a look at the molecular structure ); Step 3:

What I ended up with was an incomplete force-field modification file:
remark goes here
Li 0.000 0.000

n3-Li 0.00 0.00 ATTN, need revision

s6-n3-Li 0.000 0.000 ATTN, need revision
s6-s6-n3 39.874 100.930 Calculated with empirical ap



  Li 0.0000 0.0000 ATTN, need revision

I thought to manually edit the missing parameters by look for those among the AMBER force-field present in the software package but no parameters are reported for Lithium atom complexed within an organic molecule such as LiTFSI.

I am sure I can find some parameters from the output file of the optimisation process but what if I can only consult AMBER force-fields?

Kind regards,

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Received on Tue Dec 28 2021 - 07:30:02 PST
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