Re: [AMBER] MMPSA: PB Bomb in pb_aaradi(): ...

From: Vlad Cojocaru <>
Date: Tue, 07 Aug 2012 15:53:57 +0200


Thanks a lot for this ... Of course, we thought of going into the
fortran code but we were hesitant to actually do it. Your second tip is
quite useful (especially since you stress that this will not change any
parameters from the topology file). I guess we need to do this for all
new atom types in the ILDN modifications.

However, one mistery remains. Why using inp=2 and radiopt=0 still gives
the same error but inp=1 and radiopt=0 does not ? As far as I got it,
radiopt=0 should force to read radii from the topology file and
therefore in should work with any inp value. Or maybe when setting inp=2
the program overwrites automatically the radiopt=0 from the input file ?


On 08/07/2012 03:34 PM, Jason Swails wrote:
> On Tue, Aug 7, 2012 at 9:03 AM, Vlad Cojocaru <
>> wrote:
>> Dear Amber users,
>> We are trying to use MMPBSA (AMBER12 + AmberTools 12) to estimate the
>> binding affinity of a protein to DNA. However, when we try to use the
>> non-linear Poisson Bolzmann (npbopt=1) with the the non-polar solvation
>> free energy estimated using the cavity and dispertion terms approach
>> (inp=2), we are getting the error "PB Bomb in pb_aaradi(): No radius
>> assigned for atom 14 CG C6" (see details below). The atom is a CG in a
>> ASP (C6 atom type in the ILDN-modified ff99SB force field). Please see
>> details of the run below.
> The problem here is that the ILDN force field appears to not be frequently
> used, at least by those that work on PBSA (it's hard to keep up with all of
> the core atom types used by all of the force fields out there).
> There are 2 straightforward solutions to this issue.
> You can go through the sa_driver.F90 code (in
> $AMBERHOME/AmberTools/src/pbsa/) and add in recognition for the C6 atom
> type where you think it belongs (I think you may have to do this for
> multiple routines).
> Alternatively, you can use to change the atom type names from C6
> to C, which is the 'official' Amber force-field type for that particular
> atom (this will NOT change any parameters, just the name of the atom type).
> To take this approach, use the "change" command with the AMBER_ATOM_TYPE
> keyword (if you are using the GUI, you can use the arrow buttons to scroll
> to that key). The selection mask should be .%C6 to select all C6 atom
> types (or you can use :ASP.CG -- just make sure you capture all of the
> atoms you want to capture). Then set C as the new value.
> Now, if we use inp=2 and radiopt=0 (radii taken from the topology file;
>> we know we should not do this in principle - but we did it for testing),
>> the same error occurs.
>> However, if we use inp=1 and radiopt=0, MMPBSA runs but it gives
>> abnormal results (in the range of +4000 kcal/mol .. obviously a non-sense).
>> When we use inp=0 and radiopt=0, we get a better result (in the range of
>> -100 kcal/mol) but here we do not take into account the non-polar
>> solvation free energy
>> MMGBSA runs fine with the same system and gives reasonable values at
>> first glance (in the range of -200 kcal/mol).
>> Could anybody explain this error message? Are we doing something wrong
>> here ?
>> Also an additional question: how should we control the SASA calculation
>> in MMBSA ? ssaopt=0, saopt=0 are defaults. Does this mean that by
>> default no estimation of SASA is done since saopt=0? Does the gbsa
>> parameter play any role for MMPBSA or is used just for GB calculations ?
> gbsa does nothing except for GB calculations.
> HTH,
> Jason

Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]
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Received on Tue Aug 07 2012 - 07:00:03 PDT
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