Re: [AMBER] PrmtopError: Residue mismatch while mapping. Incompatible topology files or bad mask definitions

From: Jason Swails <>
Date: Wed, 17 Sep 2014 11:42:17 -0400

On Wed, Sep 17, 2014 at 11:33 AM, Thomas Evangelidis <>

> On 16 September 2014 19:13, Jason Swails <> wrote:
> > On Tue, 2014-09-16 at 17:05 +0300, Thomas Evangelidis wrote:
> > > Greetings,
> > >
> > > I want to run script using 3 different trajectories (complex,
> > > receptor, ligand). The difference between the receptor and the complex
> > > trajectories was that the receptor had an aspartate protonated which
> was
> > > unprotonated in the complex. This is perfectly fine in reality, but
> when
> > it
> > > attempted to use the program complained.
> >
> > This is actually not fine (at least not according to the details you've
> > written here). The MM/PBSA thermodynamic cycle does not accommodate
> > "chemical" changes (i.e., changes in covalent bonds). There is an extra
> > process of deprotonation and proton desolvation that is not accounted
> > for. So you would need to add on a thermodynamic cycle similar to the
> > kind used for pKa calculations and constant pH simulations.
> >
> > > So I modified the
> > > receptor trajectory and topology by removing the extra proton from the
> > ASP
> > > side-chain. However, I still get a residue mismatch error that may be
> > cause
> > > by the modification I introduced. Do you believe this is the case? If
> > yes,
> > > is there any work around to fix it?
> >
> > takes steps to catch errors that break the assumptions of
> > MM/PBSA analyses (like what you are doing here). [1] Simply stripping
> > the extra proton will not work -- also checks that the residue
> > sequences are the same in the bound and unbound states (ASH != ASP) and
> > it checks that the atoms have the same charges in the bound and unbound
> > states... which they won't if all you did was strip out a hydrogen atom
> > using cpptraj.
> >
> > You can use to process each trajectory independently and then
> > combine them yourself as legs of the applicable thermodynamic cycle for
> > your process.
> >
> >
> >
> Good point. The protein is a transporter with a binding pocket that becomes
> solvent exposed (outward facing conformation) when ASP51 is protonated
> (ASH51). So the receptor trajectory was actually created to monitor the
> opening of the substrate binding cavity. Deprotonation of ASH51 occurs upon
> ligand binding and triggers the occluded ==> inward facing transition. My
> purpose is to compare free energies of binding for a series of analogues
> with know kinetics. This protonation-deptonation is associated with large
> conformational changes and hence a significant entropic change which is
> impossible to estimate. So I thing my best bet is to calculate relative
> free energies between the ligands (given that the entropic cost of binding
> is quite similar for each of them) by using only the complex trajectories I
> have.

​Sounds reasonable.

I tried to do that for one complex but I am getting a series of errors of
> the following type:
> PB Bomb in pb_aaradi(): No radius assigned for atom 65 CB 3C
> PB Bomb in pb_aaradi(): No radius assigned for atom 79 CB 2C
> PB Bomb in pb_aaradi(): No radius assigned for atom 115 CG CO
> These are associated with protein atoms, which is strange since I used
> ff14sb. I tried to correct them with using:

​It looks to me like you are substituting atom names for types. I think
this should read


> Is this correct? Should all these carbons be of type 'C' ?
> ​

​I would use type CT (used to be the prototypical sp3-hybridized C used for
all Calpha's in ff99SB and earlier). C is the carbonyl type, I believe.
 Of course it may be safer to check the parameter files and see what the
3C, 2C, and CO types really are and pick the closest-matching type from
ff99SB. Although I think you can specify radiopt=0 to use the radii in the
prmtop file instead? (it doesn't appear that PBSA has updated its atom type
lists to support the new types in ff14SB).

Hope this helps,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Sep 17 2014 - 09:00:03 PDT
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