Re: [AMBER] issues with MMPBSA and explicit waters

From: Alfredo Quevedo <>
Date: Tue, 03 Sep 2013 11:09:05 -0300

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


El 02/09/2013 13:08, Jason Swails escribió:
> On Mon, Sep 2, 2013 at 10:39 AM, Alfredo Quevedo <>wrote:
>> 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
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Received on Tue Sep 03 2013 - 07:30:03 PDT
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