It's been fixed in the latest AmberTools release ... it no longer uses
any pairlist ...
Ray
On Fri, May 20, 2011 at 1:06 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?
>
> 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.
>>> _______________________________________________
>>> AMBER mailing list
>>> 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
>>_______________________________________________
>>AMBER mailing list
>>AMBER.ambermd.org
>>http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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>
>
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Received on Fri May 20 2011 - 13:30:05 PDT
