Re: [AMBER] How to turn off non-bonded interactions between non-bonded atoms?

From: Jason Swails <>
Date: Tue, 6 Dec 2011 12:03:01 -0500

On Tue, Dec 6, 2011 at 11:15 AM, Marc van der Kamp <
> wrote:
> 4ions.prmtop is attached.
> I created a modified version (i.e. with all ion-ion pairs in the exclusion
> list): 4ions_ex.prmtop (attached)
> $ diff 4ions.prmtop 4ions_ex.prmtop
> 25c25
> < 1 1 1 1
> ---
> > 3 3 3 3
> 91c91,92
> < 0 0 0 0
> ---
> > 2 3 4 1 3 4 1 2 4
> 1
> > 2 3

These modifications are not correct (and incomplete). Modifying the
topology file generally entails more than you'd expect. You have to adjust
the appropriate pointer in the POINTERS section as well as make sure that
the format (and potentially ordering) of the various sections are
consistent with what sander/pmemd expect. My general warning here is:
understanding the topology file is difficult, but successfully modifying
the topology file (in a non-trivial way) is an order of magnitude more
difficult, something I dare not do by hand even after studying the prmtop
format and the sander/pmemd code that uses it.

Did you try using parmed or xparmed to do this? (I can't remember if I
sent you the code for it). When I create a 4-Na+ system and use parmed to
add every atom to each others' exclusion list, I get the appropriate result
of 0s for every energy value (since no nonbonded interactions are
calculated and none of the atoms are bonded with one another), and I get
the "appropriate" energies for the original topology.

If you need parmed or xparmed, just let me know and I'll send it to you, or
if you need instructions on how to use it, I can provide those as well.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Tue Dec 06 2011 - 09:30:02 PST
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