RE: AMBER: &dipoles in sander

From: Ross Walker <>
Date: Sat, 22 Jan 2005 11:11:54 -0800

Dear Jenk,

> I guess I have forgotten to indicate before
> that my molecule is a small single unit (MW~300 Da).
> Isn't it just possible to define two (or one?)
> amino center(s) within the same unit using
> the &dipoles option?

I'm not sure what you mean by this. You should be able to define any group
of atoms using group input as defined in the Amber manual. So, e.g. a list
of atoms, specific residues, atoms matching a certain template etc etc.

You can define any number of groups. The information printed for each group
will be the centre of mass of that group. If you look in
$AMBERHOME/src/sander/prn_dipoles.f you will find how it works. Essentially
it finds:

Permdipx = sum(n=1->atoms in group) (charge(n)*x(n)-cmx)
Permdipx = sum(n=1->atoms in group) (charge(n)*y(n)-cmy)
Permdipx = sum(n=1->atoms in group) (charge(n)*z(n)-cmz)
Permanent dipole = sqrt((permdipx^2)+(permdipy^2)+(permdipz^2))

Where x(n) is the x coordinate of atom n and cmx is the x coordinate of the
centre of mass of that group. It also gets the induced dipole from the
inddip array. This is the internal array used by sander when running an
inducible dipole simulation. (e.g. with FF02).

Indiptotal = sqrt((inddipx^2)+(inddipy^2)+(inddipz^2))

The total dipole is then

Diptotal =

> &dipoles
> ATOM 22 12 # 22 12 are positively charged Ns
> &end

There is a couple of problems here. First of you need two END's. It is a
quirk of the way group input works but essentially you need an END after
each group and then an extra END to indicate that there are no more groups.


Group 1
ATOM 1 5

Also, you need to check the manual as I don't have it to hand at the moment
but I think

ATOM 22 12

Is not valid as this implies atoms 22 to 12. This may work but alternatively
may return an empty group. I am not sure...
Try correcting the issue of having two ENDs first and see how it goes.

> NSTEP = 0 TIME(PS) = 0.000
> rfree: End of file on unit 5

This is almost certainly due to the groups being invalid.

> If the &dipoles option is not designed to give
> dipole info (i.e.; inducable dipole) for
> intra-residual atomic groups, would it still be
> likely to utilize the EPOLZ info above to compare
> polarizabilities between different conformers of
> the same molecule?

It will give the dipole info for any group of atoms you specify. Essentially
it will give you the current inducible dipole on the system from the
simulation and the total dipole calculated with respect to the centre of
mass. The only real issue is what the dipole information means if the group
of atoms you have chosen do not sum to zero charge. This is why it gives the
information with respect to the centre of mass.

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 Jan 22 2005 - 19:53:00 PST
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