AMBER Archive (2009)

Subject: [AMBER] Lennard Jones Potential A and B coefficients in Topology file

From: Peter Schmidtke (pschmidtke_at_mmb.pcb.ub.es)
Date: Fri Oct 30 2009 - 13:32:32 CDT

Dear Amber Mailing List readers,

I would like to understand the Amber Topology file format, without looking
to Fortran Source Code of Amber. I am currently especially interested in
retrieving the A and B coefficients for the Lennard Jones 12-6 potential
(maybe 10-6 later also). I had a look and just found this :

FORMAT(5E16.8) (CN1(i), i=1,NTYPES*(NTYPES+1)/2)
  LENNARD_JONES_ACOEF : Lennard Jones r**12 terms for all possible
           atom type interactions, indexed by ICO and IAC; for atom i
           and j where i < j, the index into this array is as follows
           (assuming the value of ICO(index) is positive):
           CN1(ICO(NTYPES*(IAC(i)-1)+IAC(j))).

FORMAT(5E16.8) (CN2(i), i=1,NTYPES*(NTYPES+1)/2)
  LENNARD_JONES_BCOEF : Lennard Jones r**6 terms for all possible
           atom type interactions. Indexed like CN1 above.

First question : what is CN1, I suppose a program internal variable?

The number of atom types are respective to the forcefield or only
respective to the current structure?

I suppose that IAC corresponds to the %FLAG ATOM_TYPE_INDEX in my topology
file is coming from amber9?

Where can I find all the input files for reading the atom type indices,
CN1, CN2, ASOL, BSOL for the amber 99 ff?

As I told you I suppose I can find this in the source code, but it is quite
heavy to understand it from scratch for non insiders.

Thank you in advance.

Best regards. 

-- 

Peter Schmidtke

----------------------
PhD Student at the Molecular Modeling and Bioinformatics Group
Dep. Physical Chemistry
Faculty of Pharmacy
University of Barcelona

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