[AMBER] Explicit Solvent Constant pH MD

From: Rahul Ramesh <raramesh.umich.edu>
Date: Tue, 30 Jun 2015 16:53:13 -0400

I am using AMBER's constant pH MD to study the effect of drug on a polymer
having carboxylic acid side chain. To start off with , I am currently
trying to simulate a monomer which has a cellulose ring with a COOH group
attached. The simulation is performed using amber 14 explicit solvent
constant pH MD following Jason Swails tutorial. Since my system does not
resemble any protein residue , I modified the *residues.py *code to
incorporate my monomer. The force field used is AMBER 99 SB. The cpin file
generated looks fine. The reference energy for the protonated deprotonated
transition was obtained by performing a Thermodynamic Integration (TI) . As
a test case , I set the solvph equal to the pKa of the carboxylate side
group. While performing MD , there are no transitions between the
protonated and deprotonated states of the monomer. The system is always in
the protonated state for 2 ns.
I have four questions regarding this ,

1) As of now , I have only one titratable residue ( monomer has 35 atoms
totally ) which is initially in its protonated state , I would like to know
if ions need to be added in the system while doing explicit solvent
constant pH MD. If so how many ?

2) Is there any reason why transitions between protonated and deprotonated
wouldn't happen? Is the amber 14 constant pH MD tuned only to titrate

3) I would like to know the units of the reference energy which are given
in the python code *residues.py *

4) Suppose I want to perform this simulation in implicit solvent just in
case explicit solvent doesn't work, how can I obtain the partial charge
information for my polymer accounting for implicit solvents

Thank you
Rahul Ramesh
Graduate Student
University of Michigan Ann Arbor
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Received on Tue Jun 30 2015 - 14:00:03 PDT
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