Re: [AMBER] Can anyone tell me what the parm99.dat values correspond to?

From: <>
Date: Mon, 15 Mar 2010 20:00:34 -0400

 Okay now the first term of the wikipedia amber force is accounted 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.





-----Original Message-----
From: Bill Ross <>
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?

       - 4 - ***** INPUT FOR BOND LENGTH PARAMETERS *****

                    IBT , JBT , RK , REQ


         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


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