AMBER Archive (2006)

Subject: Re: AMBER: Mutual exclusion of atoms

From: Nitin Bhardwaj (nbhardwaj_at_gmail.com)
Date: Mon Nov 06 2006 - 16:27:49 CST

Thanks Thomas,
  That was helpful. In my specific case, I can not use Sander (or any
other Amber tool) to perform calculations for this project. I have to
use NAMD, so I need a modified prmtop file where the mutually excluded
atoms are explicitly defined. So, I was wondering what is the format
of preparing a list of mutually excluded atoms by changing the prmtop
file. Say, I want to exclude atom with atom index 1 from having any
N-B interactions with atoms having atom indexes 34 and 35 and
similarly exclude atom with index 2 from atom indexes 36 and 37, what
should be the format of saying this in the prmtop file, so that these
two sets are mutually excluded during the calculations.

I tried to look up in the formats page, but its a little complicated
and does not have any example: http://amber.scripps.edu/formats.html

Is there an example available for this kind of a prmtop file?

Thanks a lot again for your help.
Rgds,
Nitin

On 06/11/06, Thomas Steinbrecher <steinbrt_at_scripps.edu> wrote:
> Dear Nitin,
>
> > I have to build a system where I want that a set of atoms should not
> > "see" atoms from another set ie., they should be mutually excluded. I
>
> as far as I know (which might not be very far), amber does not have this
> capability. But with the free energy perturbation facilities as they are,
> a change from one molecule to another can be accomplished. You would
> set up a prmtop file for both your starting and ending states and
> simulate the transition between them. In this way the 'old' and 'new'
> molecules do not per se interact with each other, rather you have
> simulations of mixed states that have partially characteristics of one
> molecule and partially of the other.
>
> The amber9 manual p153+ explains how that is done. Be careful, if your
> molecules are very different, the amount of sampling necessary to obtain a
> converged transition might be huge.
>
> If the two compounds to compare are very different in number and types of
> atoms etc., you might need to set up your transformation as two separate
> steps. Find out the largest common scaffold of your two molecules and
> prepare thermodynamic integration calculations that change both the
> molecules you want to compare into it. Simulate these two transitions and
> sum up their results for the total dG of your two molecules.
>
> Kind Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> The Scripps Research Institute
> 10550 N. Torrey Pines Rd.
> San Diego CA 92037, USA
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