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
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Received on Fri May 20 2011 - 13:30:03 PDT
