Dear Amber community,
I am running TI simulations with sander.MPI in Amber 20. My systems are all made of a simple dipeptide in explicit TIP3P waters + ions. These simulations are intended for baseline corrections of the TI simulations I have done for the protein systems, in which I transform the charge state of residues.
I have a working TI protocol for the protein systems with similar setups. But I am having trouble getting reasonable DV/DL for these simple dipeptides. I got some very large (over 3000 kcal/mol) DV/DL because I cannot shield the charged side chain from binding with a counterion..
Please see more details below about the simulation setups:
The dipeptide is a glutamate residue capped on both sides: NME-GLU-ACE.
The protonated form is: NME-GLH-ACE
The initial state contains: NME-GLU-ACE, 4 Na+, 3 Cl-, about 23000 TIP3P waters
The end state contains: NME-GLH-ACE, 3 Na+, 3 Cl-, same number of waters
The atoms that undergo alchemical transformation are:
OE2 and one Na+ in the initial state
OE2 and HE2 in the end state
I would really appreciate any comments/suggestions regarding this… Is it just a bad idea to transform a counterion (even though I have that delta G canceled in my thermodynamic cycle..)? Should I just exclude all Na+ to avoid the binding?
Many Thanks,
Amy
--
Amy He
Chemistry Graduate Teaching Assistant
Hadad Research Group
Ohio State University
he.1768.osu.edu<mailto:he.1768.osu.edu>
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Received on Tue Mar 07 2023 - 11:00:03 PST
