Re: [AMBER] issues with MMPBSA and explicit waters

From: Alfredo Quevedo <>
Date: Tue, 03 Sep 2013 15:17:28 -0300

Thank you Jason for the help, I will inpect deeply into the output files
and go back to the list in case I can find a solution,
best regards

El 03/09/2013 15:12, Jason Swails escribió:
> 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
> complex-1-wat.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,
> Jason
> 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

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
Received on Tue Sep 03 2013 - 11:30:04 PDT
Custom Search