Re: [AMBER] setBond

From: Brian Radak <>
Date: Tue, 3 Dec 2013 12:59:47 -0500

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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Received on Tue Dec 03 2013 - 10:30:02 PST
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