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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Received on Fri Oct 30 2009 - 11:30:04 PDT
