Hi Jiapu,
> I am searching the FORTRAN codes in Amber 8 software, for getting the
> piece of FORTRAN code to calculate the ENERGY of Sander's [bonds +
> angles + dihedrals + nonbonded-paris] four terms. The force field's
> formula can be seen from http://amber.scripps.edu/eqn.txt, but the
> actual parameters for this formula cannot be known exactly from this
> website. Could you please present me some messages on how to get the
> actual FORTRAN code for this formula, with exact parameters known?
> Thanks in advance.
>
> Faithfully yours,
>
> Jiapu
This is not as easy as it might sound. The different energies are computed
in different subroutines. Check ene.f for the bond, angle and dihedral
terms, 1-4 interactions are computed in extra_pts.f. the non-bonded pairs
vdw potentials are intertwined with the Ewald electrostatics calculation,
mainly in nonbond_list.f, short_ene.f and ew_directe.h. That code is higly
optimized and parallelized, so it will take some time to understand.
For the actual parameters used in all these methods, look at the
specification of the prmtop file on the amber homepage, all the MD
parameters are listed in the prmtop in semi-humanreadable form.
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Oct 21 2007 - 06:07:37 PDT
