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
Received on Wed Aug 17 2011 - 19:30:02 PDT
