Re: [AMBER] issues with MMPBSA and explicit waters

From: Jason Swails <>
Date: Tue, 3 Sep 2013 14:12:15 -0400

I get a different error when I run your files:

$ -O -i -cp complex-1-wat.prmtop -rp
receptor-1-wat.prmtop -lp ligand-1-wat.prmtop -y 1-water.mdcrd
Loading and checking parameter files for compatibility...
sander found! Using /usr/local/amber12/bin/sander
cpptraj found! Using /usr/local/amber12/bin/cpptraj
Preparing trajectories for simulation...
1 frames were processed by cpptraj for use in calculation.

Running calculations on normal system...

Beginning GB calculations with /usr/local/amber12/bin/sander
  calculating complex contribution...
 bad atom type: f
CalcError: /usr/local/amber12/bin/sander failed with prmtop
Exiting. All files have been retained.

Same type of error, but the bad atom type is "f", not "HW". In this case,
however, both systems fail immediately with the same error. (F and Cl
radii have been assigned in the upcoming version of Amber, so both systems
finished correctly upon running with the developmental version of the
code). Look carefully at the output from and make sure that it
is using the same executables you expect it to use, and analyze the header
of the _MMPBSA_*.mdout files to make sure that the program version is 12.
 (Also make sure you've updated the installation fully and recompiled).

Until your error matches mine (which is a fully up-to-date version of the
Amber 12 release with AmberTools 13), I won't know how to help (unless you
can tell me exactly what changes you made to the underlying source code).

Good luck,

On Tue, Sep 3, 2013 at 10:09 AM, Alfredo Quevedo <>wrote:

> Dear Jason, thank you very much for you reply.
> I am using Amber12 and the module. I first considered adding
> the parameters of HW to the mdread.F90 file, but I believe that may no
> be the source of the problem, because when I use only one water molecule
> (which also has the HW atom type), the calculation finishes without any
> problem. When retaining 2 o more water molecules this problem arises.
> Also, I think that the missing parameters would also affect calculation
> on the complex, but they seem to crash when the receptor components is
> computed. I checked, and all water molecues are asigned the same atom type.
> To clearly demonstrate the problem yesterday I sent a mail with the
> files attached but they havent been approved by the moderator yet.
> Thank you very much for your support
> Alfredo
> El 02/09/2013 13:08, Jason Swails escribió:
> > On Mon, Sep 2, 2013 at 10:39 AM, Alfredo Quevedo <
> >
> >> Dear Amber users, I am facing a problem with an MMPBSA calculation when
> >> keeping explicit water molecules. The procedure I am following to
> >> perform the decomposition analysis is:
> >>
> >> 1: center and image the explicit MD trajectory,
> >> 2: use cpptraj to identify "closest" water molecules, write stripped
> >> .prmtop file and resulting trajectory,
> >> 3: generate "complex", "receptor" and "ligand" .prmtop files using
> >> (without stripping waters),
> >> 4: run the module, settinf the "strip_mask" keyword to non
> >> default parameters so as to keep explicit waters.
> >>
> >> When I performed the above mentioned procedure keeping just 1 explicit
> >> water (closest 1: in step 2), the calculation finished without any
> >> problem and calculated components seemed to be ok.
> >> My problem originates when I want to keep 2 or more explicit water
> >> molecules in the trajectory, in which when running step 4, the
> >> calculation for the complex finishes ok, but when the calculation for
> >> the receptor starts I get the error "bad atom type: HW". This error
> >> originates from sander when trying to run the decomposition calculatioin
> >> from the files created by (_MMPBSA_gb_decomp_rec.mdin,
> >> _MMPBSA_dummyreceptor.inpcrd). I inspected the generated files with VMD
> >> using receptor.prmtop and everything seems to be ok. I cant understand
> >> why sander gets an "atom type" error if everything was ok for the
> >> simmulation corresponding to the complex.
> >> Has anyone faced this problem before?.
> >>
> > This is caused by the fact that there are no parameters for gbsa=2 code
> for
> > HW atom types. Look at the relevant code in mdread.F90 [or mdread.f]
> > ($AMBERHOME/src/sander, around line 2215 or so, I think). You will need
> to
> > add code in order to assign a radius to the HW type (you should probably
> > make it the same as the other hydrogen type(s) that are defined there).
> >
> > In the future, it would be helpful to tell us what version of Amber and
> > AmberTools you are using. I don't see how you could possibly be getting
> > this error with Amber 12, so I assume you're using Amber 11 (if you are
> > using Amber 10 or earlier, will not work with decomposition).
> >
> > Good luck,
> > Jason
> >
> --
> *********************************************************
> Prof. Dr. Mario Alfredo Quevedo.-
> Laboratorio de Química Medicinal.-
> Dpto. de Farmacia - Fac. de Ciencias Químicas.-
> Universidad Nacional Córdoba.-
> 5000 Córdoba, Argentina
> TE: +54 351 5353865 Int: 53355
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Sep 03 2013 - 11:30:04 PDT
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