RE: AMBER: Which source file determine the initial value of IX XX arrray in AMBER8?

From: <>
Date: Sat, 14 May 2005 12:43:46 -0700

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

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

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

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 |
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Received on Sat May 14 2005 - 20:53:00 PDT
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