Dear Caoch
> i want to add a new energy potential(12-3 form VDW) to the
> system in
> AMBER8. i tried to understand how AMBER gets system's energy
> and force.
> In the 'subroutine bond 'it seems AMBER uses the information
> from several
> array such as IX XX IB JB to caculate energy and force.
> I guess these array get values from topology file but I don
> not know
> which source file does this work.
> I am not very simlar with AMBER and I will be very
> appreciated for any
> advice.
The prmtop file is read by rdparm.f and this fills the relevant sections of
xx(called x in rdparm) and ix with the parameters from the prmtop file.
Note, you may find it easier to simply modify the existing 12-6 potential in
sander rather than creating an "extra" option. If you modify the original
you can simply build yourself 2 executable files, one that uses 12-6 and one
that uses 12-3.
If you are doing gas phase or periodic boundaries you will need to modify
the subroutines:
ew_directe.h -> This contains the code for the 12-6 VDW and is included in
sections of short_ene in ew_direct. Don't forget to update both the energy
and the derivative terms here.
You will also need to update do_14_cg() in extra_pts.f - this is responsible
for doing the scaled 1-4VDW interactions - see line 1518 and 1556 of
extra_pts.f
If you are doing induced polarisation then you need to modify
short_ene_dip() in ew_direct.f and do_14_dipole() in extra_pts.f - see line
1685.
If you are doing generalised born then you will need to modify egb.f see
line 699
Note, there may be some other places you need to modify that I didn't find
when quickly scanning through.
What I suggest you do is start with a simple gas phase case that you can
solve analytically on paper. Then modify sander and make sure you get out
the answer you expect.
I hope this helps
All the best
Ross
/\
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|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 |
| EMail:- ross.rosswalker.co.uk |
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Received on Sat May 14 2005 - 20:53:00 PDT
