[AMBER] Problem of PB calculation when running mmpbsa.py

From: bin wang <wang_p_z.yahoo.com.cn>
Date: Sat, 21 May 2011 03:36:29 +0800 (CST)

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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Received on Fri May 20 2011 - 13:00:04 PDT
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