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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Received on Sat Sep 18 2010 - 08:00:04 PDT
