Hi Bill and Lachele,
Thank you very much. So dummy atoms exist just because internal coordinates
system instead of Cartesian coordinates system is used.
I think the GLYCAM prep file contains all the sugar building blocks, and I
just want to dig all the parameters from the prep file.
But since there are ideal bond lengths, angles, and dihedral angles
parameters, where can I find the corresponding values of force constants as
in the functional forms (potential energy equations) of amber force field?
Yun
On Wed, Aug 17, 2011 at 7:09 PM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
> The prep file format is a little confusing at first.
>
> > But I do not understand what are those first three DUMM atoms for?
>
> Those set the coordinate space.
>
> > What -0.1940 stands for?
>
> The manual recommends not using this number at all, so in Glycam prep
> entries, we use the space as a convenient location indicate the total
> charge on the residue. And, we don't use it for any other purpose.
>
> > What are the letters and numbers from 4th to 7th columns mean?
>
> Of these, only column 4 is used. 5-7 are completely ignored by most
> programs (this is stated in the docs). The numbers are, essentially,
> comments regarding the atoms to which the bonds, angles and torsions
> apply. However, since they are never used, any incorrect entries in
> those columns are unlikely to have ever been caught. The atoms to
> which the bond lengths, angles and torsions are applied must be
> deduced by inspecting the contents of column 4. To understand column
> 4, go see the page that Bill referenced. If you're a CS person, I am
> told that if you consider it a stack, and you count up from the
> bottom, the entries in column 4 are a bit easier to make sense of.
>
> :-) Lachele
>
>
> On Wed, Aug 17, 2011 at 9:34 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >> Or could anyone just direct me to the right documentation to read?
> >
> > Searching google for 'amber prep file':
> >
> > http://ambermd.org/doc/prep.html
> >
> > Bill
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Aug 18 2011 - 11:30:03 PDT
