Re: [AMBER] Explicit Solvent Constant pH MD

From: Jason Swails <>
Date: Thu, 9 Jul 2015 12:49:38 -0400

On Thu, Jul 9, 2015 at 12:42 PM, Rahul Ramesh <> wrote:

> Thank you Jason for the wonderful inputs. I'm currently working on the
> aspartic acid residue and I would like to know the charge methods you used
> to derive those charges and also which force field is used? I calculated my
> partial charges using acpype which uses bcc and amber 99SB forcefield?

​The exact process used to derive the charges is to assign the backbone
charges according to the protonated form (in this case, the neutral
aspartate). Then the side-chain charges are set to the charges assigned in
the given protonation state (you can see these charges in the
all_amino94.lib file). The difference in backbone charges between the
protonated and deprotonated states is then added to the beta-carbon of the
deprotonated state to make sure that the net charge is always correct. The
underlying force field is FF99SB.

This is done because the backbone charges *have* to be the same for each
state, otherwise the scaled 1-4 electrostatic terms will make the reference
energy sequence dependent.

Using antechamber (which I think is what acpype does behind the scenes) is
the wrong approach here.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Thu Jul 09 2015 - 10:00:03 PDT
Custom Search