[AMBER] MM_PBSA analysis warning

From: Sangita Kachhap <sangita.imtech.res.in>
Date: Wed, 13 Jul 2011 17:00:09 +0530 (IST)

Hello all

I am MMPBSA analysis of protein-DNA complex using perl script of amber11.
I have successfully completed binding energy calculation. But when I visualize
log file ther are some warning

    WARNING: Missing PBCAV for PB in 728 -> Taken from 727
    For details see:
http://ambermd.org/Questions/mm_pbsa.html#check_completeness_missing_var_taken_from
    WARNING: Missing PBDIS for PB in 728 -> Taken from 727
    For details see:
http://ambermd.org/Questions/mm_pbsa.html#check_completeness_missing_var_taken_from
    WARNING: Missing SURF for MS in 728 -> Taken from 727


As well as it skipping some calculation like:

 No values for MM_ELE existing -> Skipping
 No values for GB_GBSOL existing -> Skipping
 No values for MM_GAS existing -> Skipping


Will these affect the final calculated energy?


With regards
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH


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Received on Wed Jul 13 2011 - 04:30:04 PDT