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

From: Jason Swails <>
Date: Tue, 6 Dec 2011 14:50:56 -0500

On Tue, Dec 6, 2011 at 12:16 PM, Marc van der Kamp <
> wrote:

> Thanks Jason!
> I should have figured it wouldn't be all that easy to manually edit the
> prmtop.
> Yes, you did sent me parmed, thanks! I looked through the information of
> how to use it, and had a project student (for whose project this is) try it
> out. She used the following input (
> #Add exclusions to the exclusion list so that non-bonded interactions
> between mask1 and mask2 atoms are not computed.
> addExclusions :Na+ :Na+,Cl-
> addExclusions :Cl- :Na+,Cl-

You could combine these 2 into

addExclusions :Na+,Cl- :Na+,Cl-

It would be helpful to put the command "printDetails :Na+,Cl-" to see what
atoms are selected by the masks.

Also, can you send me the 2 topology files? (exclusions2.prmtop and the
original) so I can compare them? This was the same command I used
successfully in the email I sent above.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Tue Dec 06 2011 - 12:00:03 PST
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