Dear all,
It turns out that it had something to do with the Calcium cation (Ca2+) in
the analyzed system. I applied the mbondi2 for the PBRadii of all the atoms
in the system. After I excluded Calcium cation from the MMPBSA analysis,
this PB Bomb error disappeared.
I checked the modified Bondi radii in the prmtop file and found that the
atomic radii for Calcium cation was 1.7. This is small compared to the vdw
radii of Calcium atom (2.0). I guess that might be the problem. I tried to
increase the radii of Calcium cation to something like 2.0 or 2.7. Still the
PB Bomb error exists!
So now my question turns to that how I could get appropriate PBRadii for
Calcium cation (or some other metal ions) if I would like to include them in
the mmpbsa analysis? I searched in the mailing list and found nothing
related to this question.
Any suggestions would be greatly appreciated !
Kind regards,
Qiong
*************************************
Qiong Zhang
Department of Theoretical Chemistry
School of Biotechnology Royal
Institute of Technology
Roslagstullsbacken 15
SE-10691 Stockholm, Sweden
*************************************
I checked the reference for the mbondi2 [Onufriev, A.; Bashford, D.; Case,
D.A. Exploring protein native states and large-scale
conformational changes with a modified generalized Born model. Proteins,
2004, 55, 383–394.]
On Tue, Oct 25, 2011 at 11:07 AM, Qiong Zhang <qiong.zhang.qzh.gmail.com>wrote:
> Dear all,
>
> I am doing test mmpbsa runs with mmpbsa.py in the lastest Ambertools1.5
> (the latest bugfix.all have been patched!)
>
> My input files read:
>
> Input file for running PB
> &general
> startframe=1, endframe=3, interval=1, receptor_mask=":2-390",
> ligand_mask=":1",
> verbose=2, strip_mdcrd=0, entropy=0, use_sander=0, netcdf=0
> /
> &pb
> indi=1.0, exdi=80.0, scale=2.0, linit=1000, prbrad=1.4,
> istrng=0.00, inp=1, cavity_surften=0.00542, cavity_offset=-1.008,
> fillratio=4.0, radiopt=0, sander_apbs=0
> /
>
>
> With the parameter fillratio either equal to 4.0 or 2.0, I had this error:
>
> Beginning PB calculations with mmpbsa_py_energy...
> calculating complex contribution...
> PB Info in pb_read(): npopt has been overwritten with inp
> Total surface charge 1.9610
> Reaction field energy -3269.5089
> Cavity solvation energy 79.8421
> * PB Bomb in pb_atmlist(): maxnba too short*
>
> I searched the mailing list, found this similar error:
> http://archive.ambermd.org/201107/0127.html , but no solution....
>
> Could you please give me some hint on how to solve this problem please?
>
> Huge thanks in advance !
>
> Qiong
>
> *************************************
> Qiong Zhang
>
> Department of Theoretical Chemistry
> School of Biotechnology Royal
> Institute of Technology
> Roslagstullsbacken 15
> SE-10691 Stockholm, Sweden
> *************************************
>
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Received on Tue Oct 25 2011 - 05:30:03 PDT
