AMBER Archive (2006)

Subject: Re: AMBER: single or dual topology for TI?

From: Holly Freedman (freedman_at_phys.ualberta.ca)
Date: Sat Oct 21 2006 - 15:32:42 CDT

Thanks , David. Should I follow a similar procedure when creating atoms, ie when going from OCH3
to OCH2CHCH2, should I first create atoms without charges from dummy atoms, and then in another
cycle add the charges to new atoms?

Holly

> Holly,
>
> > I plan to use AMBER8 to set up some thermodynamic integration calculations for determining
relative
> > free energies of colchicine (a three-ring, 54 atom organic molecule) and various derivatives in
water. I
> > would like to know if the TI implementation coded in AMBER8 works better for single or
> > dual topology TI. I am going to set up TI where an OCH3 group (all atom representation) on
colchicine
> > is mutated to an OH group, or as another example, to an OCH2CHCH2 group, and I was
wondering if I
> > should use dual or single topology perturbation. For example in the first case I gave of
mutating OCH3
> > to OH, should I change that C on colchicine into an H and the three H's into dummy atoms, or
should I
> > change all atoms in the CH3 group into dummy atoms and then also have a dummy atom on the
> > colchicine that I change into an H? I've never done TI before, and it would be great to hear any
advice
> > you have on this.
>
> My personal opinion is that deleting or inserting atoms is a lot more
> "work" than any other kind of a transformation (in the sense that it
> requires more sampling to get reliable results) so it is preferable to
> do as few deletions/insertions as possible in any transformation.
> Hence, I would do it by changing the CH3 into H (changing C->H and
> deleting three hydrogens). The other important point is to make sure
> you never have charges on atoms that are being deleted, so I usually
> prefer to do a separate transformation to turn off charges on the
> atoms I'm deleting before I do the deletion (i.e. first turn off the
> charges on the H3).
>
> Best wishes,
> David Mobley
> UCSF
>
> > Thanks,
> > Holly Freedman
> > --
> > Department of Physics, University of Alberta
> > Edmonton CANADA
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu 

--
Department of Physics, University of Alberta
Edmonton CANADA

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu