AMBER Archive (2005)

Subject: RE: AMBER: &dipoles in sander

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Fri Jan 28 2005 - 04:04:21 CST

Hi Ross,

The dipoles option now works with an extra END.
One more question though:

Is it possible to measure inducable dipoles in
implicit solvent environments rather than polarized
explicit solvent environments ?

Thanks.

Jenk.

--- Ross Walker <ross_at_rosswalker.co.uk> wrote:

> 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 =
>
sqrt((permdipx+inddipx)^2+(permdipy+inddipy)^2+(permdipz+inddipz)^2)
>
> > &dipoles
> > GROUP1 1-1 MOL->MOL
> > ATOM 22 12 # 22 12 are positively charged Ns
> > END
> > &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.
>
> So:
>
> &dipoles
> Group 1
> ATOM 1 5
> END
> END
> &end
>
> 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
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 |
> | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available
> on request |
>
> Note: Electronic Mail is not secure, has no
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>
>
>
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