Dear Ray,
Thank you very much for your kind help!
For this PB Bomb problem, 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 would like to ask if the PB Bomb error is caused by the inappropriate
PBRadii for the Calcium cation? I checked the modified Bondi radii in the
prmtop file and found that the atomic radii for Calcium cation was 1.7.
Any suggestions would be greatly appreciated !
Kind regards,
Qiong
On Tue, Oct 25, 2011 at 6:31 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> Dear Qiong,
>
> I'm forwarding your email to MJ, who resolved a similar issue before
> in the previous release ... let's see what he has to say about your
> case ...
>
> All the best,
> Ray
>
> On Tue, Oct 25, 2011 at 5:13 AM, Qiong Zhang <qiong.zhang.qzh.gmail.com>
> wrote:
> > 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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Received on Tue Oct 25 2011 - 10:00:06 PDT
