For ACPYPE, consider
https://code.google.com/p/acpype/wiki/UserChargeOptions
and then
http://q4md-forcefieldtools.org/REDServer-Development/
Alan
On 9 July 2015 at 17:49, Jason Swails <jason.swails.gmail.com> wrote:
> 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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>
--
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
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Received on Thu Jul 09 2015 - 14:00:02 PDT
