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.
Regards,
Brian
On Tue, Dec 3, 2013 at 12:44 PM, Aronica, Pietro <
pietro.aronica07.imperial.ac.uk> wrote:
> Hello,
> I'm having some problems with parmed.py. I used the setBond command to
> change the length and force constant of a certain bond, and then saved the
> resulting prmtop. However, parmed.py 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
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Tue Dec 03 2013 - 10:30:02 PST
