AMBER Archive (2009)

Subject: [AMBER] mm_pbsa problem

From: Giorgos Lamprinidis (lamprinidis_at_pharm.uoa.gr)
Date: Mon Mar 30 2009 - 05:02:07 CDT

Dear al,

I hgave amber v10.
I am trying to run a MMPBSA job using as a patern the A3 Advanced Tutorial. At the last step, when i want to create the snapshot_statistics.out file i get the next warning message for all the snapshots:
=>> Reading files
    Reading snapshot_com.all.out
    WARNING: Missing PBNONPOL for PB in 0 -> Taken from -1
    WARNING: Missing ELRAELE for PB in 0 -> Taken from -1
    WARNING: Missing EPB for PB in 0 -> Taken from -1
    WARNING: Missing PBNONPOL for PB in 1 -> Taken from 0
    WARNING: Missing ELRAELE for PB in 1 -> Taken from 0
    WARNING: Missing EPB for PB in 1 -> Taken from 0
....................................
and then the calculation stops on,
=>> Calc delta from raw data

i thougt there was something wrong with my codes so i downloaded all the out files from the tutorial and i tried to run the tutorial's last calculations, to reproduce the snapshot_statistics.out from the Tutorial. I got the same messages.....
I searched alot on the amber mailing list. I saw many threads about that issues but i didn't find any reply with solution.

Can you help me what is wrong?

Regards
Dr. George Lamprinidis
School of Pharmacy
University of Athens
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