dear all,
I am calculating binding free energy using MMPBSA.py for
quadruplex-ligand system using the below given input file:
Input file for running PB and GB in serial
|&general
| endframe=100, interval=1, keep_files=0, strip_mask=:WAT, Na+,
|/
|&gb
| igb=2,
|/
|&pb
| istrng=0.000, exdi=80, indi=1.0,
| inp=1, cavity_surften=0.00542, cavity_offset=0.92,
| fillratio=4, scale=2.0, prbrad=1.4, radiopt=0,
|/
All calculation went well. But when i checked the output file, a
warning was printed
"WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL
TERMS. THE VALIDITY OF THESE RESULTS ARE HIGHLY QUESTIONABLE"
I want to know that is there any serious problem with the result or
its just a warning. The output file is attached here.
Looking forward for your responce and suggestions.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 10 2014 - 06:00:03 PDT
