Dear Alessandro and Jason,
Thanks for your immediate reply
Regards
Aneesh
On Sat, Sep 18, 2010 at 10:32 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Alessandro is completely correct. The factor of 18.2223 is multplied into
> all of the partial atomic charges to incorporate "k" from the electrostatic
> potential formula k*q*q/r so that only 2 numbers have to be multiplied, and
> that the resulting energy is in kcal/mol. A lot of the data that is in
> parameter and library files are transformed when the prmtop is written for
> runtime efficiency. For example, the van der waals radii and well depths
> are combined before being put into the prmtop file as ACOEF and BCOEF. If
> you want to look at the "human-readable" parameters, you should use the
> rdparm program to query parts of a prmtop.
>
> Hope this helps,
> Jason
>
> On Sat, Sep 18, 2010 at 8:35 AM, Alessandro Nascimento <
> al.s.nascimento.gmail.com> wrote:
>
> > That's exactly the same thing! Remember that in order to get atomic
> > charges in electron units from a PRMTOP file you muste divide the
> > value you see there (-1.41423270E+01) by 18,2223. The 18,2223 comes is
> > a conversion parameter to get Coulomb energies in kcal/mol.
> >
> > You might want to have a look at this http://ambermd.org/formats.html
> >
> > Hope that helps,
> >
> >
> > --Alessandro
> >
> > On Sat, Sep 18, 2010 at 7:26 AM, aneesh cna <aneeshcna.gmail.com> wrote:
> > > Dear users,
> > >
> > > I am using leap programme in Amber tools 1.4 for
> generating
> > > topology (parmtop) file for DNA with ' parmbsc0 ' force field. I was
> > > looking for the atomic point charges amber assigned for the back bone
> > > phosphate oxygen atoms in the topology file. In the topology file
> atomic
> > > charge on Oxygen is found to be ' -1.41423270E+01' , but in the
> library
> > > file ' all_nucleic94.lib' charge on Oxygen is ' -0.776100 ' . Why
> this
> > > difference in atomic charge?
> > >
> > >
> > > Thanks in advance
> > >
> > > Sincerely
> > > Aneesh
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > [ ]s
> >
> > --alessandro
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Sep 19 2010 - 21:30:03 PDT
