Re: [AMBER] setBond

From: Aronica, Pietro <>
Date: Tue, 3 Dec 2013 19:43:17 +0000

The manipulations are done by removing specific dihedrals with the deleteDihedrals command, so that atoms that should not see each other but do because of their 1,4 connectivity have this interaction deleted.
Using the first fix outlined in the previous email, the returned prmtop is unchanged (save, of course, for the timestamp), while the second one gives the same exclusion list reshuffling as with my original command. I'm about to send the files privately.

-----Original Message-----
From: [] On Behalf Of Jason Swails
Sent: 03 December 2013 19:23
To: AMBER Mailing List
Subject: Re: [AMBER] setBond

On Tue, 2013-12-03 at 14:04 -0500, Jason Swails wrote:
> On Tue, 2013-12-03 at 18:25 +0000, Aronica, Pietro wrote:
> > 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 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.

I think I may have misinterpreted this part of your email the first time around. Does the above ("delicate prmtop manipulations") mean that you have already used "addExclusions" in a previous ParmEd session to add exclusions to your original topology file? If so, then any "topology recalculation" will destroy those previously-defined exclusions. (The exclusion list is not processed when it is read from the prmtop, it is merely recreated when the topology changes). The changes made by "addExclusions" will persist for the entire ParmEd session, but not for any future ones.

I hadn't thought about this issue before. A few things to note here:
sander and pmemd ignore the exclusion list stored in the topology file for PME (explicit solvent) calculations---they simply regenerate the exclusion list from the bonds, angles, and torsions. The GB calculations in sander and pmemd _do_ obey the exclusion list stored in the prmtop.

> If you send me your prmtop file and your inpcrd file I will try to
> take a look.

If you do send me the files, please send it privately. I forgot to mention that.

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Tue Dec 03 2013 - 12:00:03 PST
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