Re: [AMBER] setBond

From: Aronica, Pietro <>
Date: Tue, 3 Dec 2013 18:03:14 +0000

I'm not adding a bond; I'm changing an existing bond's parameters. Connectivity is not changed, and no new dihedrals or angles or anything else are made. As far as I can tell, the two systems should have the same exclusion list.
Kind regards

-----Original Message-----
From: [] On Behalf Of Brian Radak
Sent: 03 December 2013 18:00
To: AMBER Mailing List
Subject: Re: [AMBER] setBond

By default, AMBER puts all atoms with 1-2 and 1-3 connectivity in each other's exclusion list. Atoms with 1-4 connectivity also have special, scaled non-bonded interactions. Therefore, if you add a bond where one did not exist before, you are also changing the non-bonded interactions. I don't know if this can be turned off in parmed.

Remember, you can always add a simple NMR restraint on a distance, and this will only be additive with the force field, it will not modify the non-bonded interactions in any way.


On Tue, Dec 3, 2013 at 12:44 PM, Aronica, Pietro <> wrote:

> Hello,
> I'm having some problems with I used the setBond command to
> change the length and force constant of a certain bond, and then saved
> the resulting prmtop. However, didn't just change the bond,
> but also modified the exclusion list in a way that makes the prmtop
> unusable and not working. I don't understand how changing the
> parameters of a bond should affect the exclusion list. Why is it doing this? Is there a workaround?
> Kind regards
> Pietro
> _______________________________________________
> AMBER mailing list

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 Brian Radak                                             :     BioMaPS
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