A premise: I'm working with an experimental protocol that requires a lot of custom residue and atom types and precise manipulation of the prmtop files. It has been described as "a prmtop-based FEP scheme" by Jason himself, and that's not far from the truth. Because of the settings of my system, it is crucial that the exclusion list is kept the way I originally make it in order to avoid instabilities and failures. Indeed, I manually edited the prmtop files to change only the bond length I needed to modify (which is what I expected parmed.py to do) and the issue disappeared.
The command is as follows:
setBond :MKN.CH :MKA.CG 340 1.526
setOverwrite
parmout Solv_100_0.prmtop
There's a few more, varying from 10_90 to 100_0, with different values for the equilibrium distance and the force constant. In each case, the bond parameters are correctly modified, but in addition the number of excluded atoms goes from 28762 to 28755. I'm wading through the exclusion list to pinpoint the change, but it arises from the custom residue where the bond is modified. That is the only instance of the bond in the system.
I figure it's probably my delicate prmtop manipulations that are causing this, but I don't understand why the setBond command should touch the exclusion list at all if the bond is already there and connectivity is unchanged.
Kind regards
Pietro
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf Of Brian Radak
Sent: 03 December 2013 18:08
To: AMBER Mailing List
Subject: Re: [AMBER] parmed.py setBond
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
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> 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 - 10:30:04 PST
