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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Received on Tue Oct 25 2011 - 10:00:04 PDT
