On Fri, May 20, 2011 at 4:06 PM, Zheng, Zhong <Zhong.Zheng.stjude.org>wrote:
> Actually I'm struggling with the same problem for the last couple of days.
> I am doing a MMPBSA calculation on protein-ligand binding. I have a big
> system with more than 700 residues plus counter ions and waters.
> The gb run finished ok. But the pb run never works for me. The error
> message at the end of the _MMPBSA_*.mdout is something like this:
> PB bomb in pb_reslist(): maxnbr too small
>
> I did some search online. One post typically said "The error message shows
> that the estimation of maximum pairs for
> residue-based cutoff is too small. A larger cutoff, for example by setting
> cutres=12 (default 10) usually works fine." It seems you can go change the
> code, recompile and fix this. There posts are relatively old. I'm
> wondering if amber11 has actually fixed these problems already.
> Also I'm working on a cluster and I don't have the authorization to touch
> the code as Amber is installed in public directory. So besides installing
> the ipbsa, which I can't do either, are there other options?
>
Not really... You could request that the powers that be install sander.APBS
(instructions are on the web) and use this PB solver instead, but if
modifying cutres doesn't work, you'd need to modify code to get it to work
(or install sander.APBS).
HTH,
Jason
>
> Many thanks.
>
> Agnes
>
> On 5/20/11 2:41 PM, "Bill Miller III" <brmilleriii.gmail.com> wrote:
>
> >What did your MMPBSA.py input file look like? Also, there should have been
> >some _MMPBSA_*_pb.mdout files created for the complex, receptor, and
> >protein. My guess is there are some helpful information/messages in those
> >files.
> >
> >-Bill
> >
> >On Fri, May 20, 2011 at 3:36 PM, bin wang <wang_p_z.yahoo.com.cn> wrote:
> >
> >> Hello Amber users,
> >> When I use mmpbsa.py to calculate binding energy of a protein-protein
> >> interaction, the result.dat file only showed the GB part but not the PB
> >> part.
> >> The messages are listed as follows:
> >>
> >> ptraj found! Using /opt/amber11/bin/ptraj
> >> sander found! Using /opt/amber11/bin/sander (serial only!)
> >>
> >> Preparing trajectories with ptraj...
> >> 50 frames were read in and processed by ptraj for use in calculation.
> >>
> >> Starting sander calls
> >>
> >> Starting gb calculation...
> >>
> >> Starting pb calculation...
> >>
> >> Error: No potential terms in sander output! Check output files.
> >> NOTE: All files have been retained for debugging purposes. Type
> >>MMPBSA.py
> >> --clean to erase these files.
> >>
> >> When I caculated a protein-DNA interaction, the result showed both PB
> >>and
> >> GB,
> >> but for this one, it only showed GB. I don't know what could possibly
> >> cause
> >> this problem. Need your help. Thank you.
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> >--
> >Bill Miller III
> >Quantum Theory Project,
> >University of Florida
> >Ph.D. Graduate Student
> >352-392-6715
> >_______________________________________________
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> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri May 20 2011 - 13:30:05 PDT
