Thank You, I realized that for the Aspartate residue in residues.py , the
COOH group is quite different because the two oxygens are connected to two
hydrogens each. How do I go about generating the prmtop and inpcrd file as
xleap wouldn't recognize the case where oxygen is connected to two
hydrogens and a carbon atom.
I tried an alternate method of generating the partial charges for the
backbone and CH3COOH group separately and manually entered the partial
charges in a mol2 file and then used acpype to generate the prmtop and
inpcrd file. There were lot of zeroes in the prmtop file as some of these
atom types weren't recognized. I tried generating a cpin file (just to
try), cpinutils.py did not throw any error but the cpin file was blank.
Rahul Ramesh
Masters Student
Department of Chemical Engineering
University of Michigan Ann Arbor
(+1 734-680-4453)
On Thu, Jul 9, 2015 at 4:47 PM, Alan <alanwilter.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Jul 10 2015 - 15:00:09 PDT
