On Tue, Aug 7, 2012 at 9:03 AM, Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de> 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 xparmed.py 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
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Aug 07 2012 - 07:00:03 PDT
