AMBER Archive (2005)

Subject: AMBER: question about mmpbsa

From: cui wei (ethercui_at_gmail.com)
Date: Tue Dec 13 2005 - 01:33:08 CST

I run mm_pbsa after md ,but it failed, the output tell me that pbsa not
successsful. and the out file side that

======== PB Initialization ========

     Max PBMD Nonbonded Pairs: 2228620 1176605

 PB bomb in pb_aaradi(): ZERO sigma found for non-hydrogen atom

some one told me that means there are something wring with my molecular, i
lose a sigma bond between tow heavy atom.

but in fact i have finished a MD modeling allready

my question is what is PB bomb?
what's wrong with my MM_PBSA and how to fix it ?

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