Re: [AMBER] Incorrect Bond Assignment in AMBERTools 12 LeAP

From: Aron Broom <>
Date: Tue, 16 Oct 2012 14:40:04 -0400

Yeah, I guess I'll have to check more thoroughly the process I used to make
those files.

I made a (GLY-ALA)x5 decapapetide, and the bonds were properly restrained.
It was only within the context of my full length protein that this wasn't

I'll check with AMBER as you suggest. I suspected it would probably take
more thorough work, but hoped maybe it was a known issue.

I'll report back once I've nailed down the issue.


On Tue, Oct 16, 2012 at 1:15 PM, Jason Swails <>wrote:

> On Tue, Oct 16, 2012 at 12:59 PM, Aron Broom <> wrote:
> > I recently used tleap within AMBER tools version 12, to generate some
> > protein parameter files, using AMBER_FF12SB.
> >
> > The command structure was:
> >
> > > set default PBradii mbondi2
> > > model = loadpdb protein.pdb
> > > saveamberparm model protein.prmtop protein.inpcrd
> >
> > Everything seemed to be working fine, but in trying to troubleshoot a
> > temperature problem I was having with OpenMM, I realized that some of the
> > glycine (CA-HA2 and CA-HA3) bonds were not being properly constrained.
> It
> > looking at the .prmtop file, it looks as though those bonds were not
> added
> > to the BONDS_INC_HYDROGEN list.
> >
> This would shock me. If you create a sequence ACE-GLY-NME in leap and save
> the prmtop, you can clearly see the CA-HA2 and CA-HA3 bonds in the
> BONDS_INC_HYDROGEN section. In this case, I would be less likely to
> suspect tleap than OpenMM (tleap is significantly older and more thoroughly
> tested).
> I haven't done any of the bugfixes for ambertools 12, but I don't see
> > anything about that listed. Is this something that anyone else has seen?
> > I haven't done a rigorous test to ensure it is reproducible, thought I
> > would see if anyone else has noted this kind of problem before. As an
> FYI,
> > the input pdb files I was using don't have hydrogens at all, so there
> > shouldn't have been any problem with LeAP not recognizing the atom name.
> >
> What happens if you run it through sander or pmemd? Sander reports the DOF
> in your system, properly adjusted for SHAKE constraints. Therefore, you
> should be able to use sander with "noshakemask" targeting the problematic
> residues and see if the DOF changes between the two simulations. If the
> DOF changes, then sander knows to SHAKE them, further suggesting OpenMM as
> the culprit.
> HTH,
> Jason
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
AMBER mailing list
Received on Tue Oct 16 2012 - 12:00:03 PDT
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