I don't think wikipedia is what you want to be using here. the Amber web
site has much more info, yet you keep referring to wikipedia.
parm99.dat is for all terms except electrostatics, which are assigned for
each atom, so it really depends on what you want to lok at. the library
files for the amino acids have them. did you download the entire set of
files from the Amber page?
On Mon, Mar 15, 2010 at 8:00 PM, <whimsica.aol.com> wrote:
>
> Okay now the first term of the wikipedia amber force is accounted for...ie
> Bonds.
>
> What about all the other parameters necessary to compute angles, torsions,
> electrostatics and vanderwalls?
>
> And how did you know that
> parm99.dat was for Bonds? There is nothing to suggest that in the file
> itself.
> There is no header before it starts listing values. I'm just looking at the
> file
> opening it with a text editor. Are you looking at it with a different
> method?
>
> Thanks and keep the info coming 1/6 accounted for now.
>
> Dan
>
>
>
>
>
>
>
>
> -----Original Message-----
> From: Bill Ross <ross.cgl.ucsf.edu>
> To: amber.ambermd.org
> Sent: Mon, Mar 15, 2010 2:11 pm
> Subject: Re: [AMBER] Can anyone tell me what the parm99.dat values
> correspond to?
>
>
> > So far people have just refered me to the documentation.
> > I have looked through the docs and the file specification
> > and there is not enough information to let me know what the values are.
> >
> > Here is a line example from parm99.dat
> > C -CT 317.0 1.522 JCC,7,(1986),230; AA
> >
> > What are these numbers?
>
> http://ambermd.org/formats.html#parm.dat
>
> - 4 - ***** INPUT FOR BOND LENGTH PARAMETERS *****
>
> IBT , JBT , RK , REQ
>
> FORMAT(A2,1X,A2,2F10.2)
>
> IBT,JBT Atom symbols for the two bonded atoms.
>
> RK The harmonic force constant for the bond "IBT"-"JBT".
> The unit is kcal/mol/(A**2).
>
> REQ The equilibrium bond length for the above bond in
> angstroms
>
> The input is terminated by a blank card.
>
>
> See if you can generalize from that to understand the rest of parm.dat
> format.
>
> Bill
>
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Received on Mon Mar 15 2010 - 17:30:05 PDT
