On Thu, Jul 9, 2015 at 12:42 PM, Rahul Ramesh <raramesh.umich.edu> 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.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Jul 09 2015 - 10:00:03 PDT
