So for example, I saw in the GLYCAM_06.prep file
...
22 C6 CG 3 19 15 11 1.540 109.2 -179.8 0.0230
23 H61 HC E 22 19 15 1.070 109.5 60.1 0.0000
24 H62 HC E 22 19 15 1.070 109.5 -179.9 0.0000
25 H63 HC E 22 19 15 1.070 109.5 -59.9 0.0000
...
which indicates the CG-HC bond length in a rhamnose residue is 1.070 A. But
in the Glycam_06g.dat file,
...
CG-HC 340.0 1.090 Parm94
...
it is 1.090 angstrom. So which one should be correct? Or which one would be
used as I load a rhamnose residue in tleap?
Thanks,
Yun
On Thu, Aug 18, 2011 at 11:54 AM, Lachele Foley (Lists)
<lf.list.gmail.com>wrote:
> The distances, etc., in the prep file are optimized for the whole
> residue. If you want to see the individual bond, angle, torsion
> (etc.) parameters, you need the parameter file. The most recent
> version for glycam is Glycam_06g.dat. You can find these and other
> parameters in $AMBERHOME/dat/leap/parm
>
>
> On Thu, Aug 18, 2011 at 2:03 PM, Yun Shi <yunshi09.gmail.com> wrote:
> > 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
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Aug 18 2011 - 12:30:03 PDT
