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:
ambermd.org
What I ended up with was an incomplete force-field modification file:
remark goes here
MASS
Li 0.000 0.000
BOND
n3-Li 0.00 0.00 ATTN, need revision
ANGLE
s6-n3-Li 0.000 0.000 ATTN, need revision
s6-s6-n3 39.874 100.930 Calculated with empirical ap
DIHE
IMPROPER
NONBON
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,
Damiano
This message and any attachment are intended solely for the addressee
and may contain confidential information. If you have received this
message in error, please contact the sender and delete the email and
attachment.
Any views or opinions expressed by the author of this email do not
necessarily reflect the views of the University of Nottingham. Email
communications with the University of Nottingham may be monitored
where permitted by law.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Dec 28 2021 - 07:30:02 PST
