Ok, that actually does sound like unexpected behavior. Hopefully Jason will
see this and respond.
Can you post the parmed script/commands? I'm sure that will help.
Regards,
Brian
On Tue, Dec 3, 2013 at 1:03 PM, Aronica, Pietro <
pietro.aronica07.imperial.ac.uk> wrote:
> 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
> Pietro
>
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of Brian Radak
> Sent: 03 December 2013 18:00
> To: AMBER Mailing List
> Subject: Re: [AMBER] parmed.py 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.
>
> 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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > 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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>
--
================================ 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 - 10:30:03 PST
