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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>
--
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 - 13:00:05 PDT
