AMBER Archive (2009)

Subject: [AMBER] MM - PBSA problem

From: musa özboyacı (musaozboyaci_at_gmail.com)
Date: Thu Jan 22 2009 - 11:06:54 CST

Dear Amber users,
I've trying to use mm-pbsa tool of AMBER, and everytime I use I get the same
error. I tried every possible suggestions in the old mails. However I
couldn't fix the problem. I would be very glad if you help me. Here is my
output:

=>> Values of global variables
    TEMP = 300
    R = 8.314
    gammaP = 0.00542
    betaP = 0.92
    gammaG = 0.0072
    betaG = 0
=>> Reading input
=>> Reordering files
    Final order:
    1. qq2_com.all.out: -
    2. qq2_rec.all.out: -
    3. qq2_lig.all.out: -
=>> Reading files
    Reading qq2_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
    WARNING: Missing PBNONPOL for PB in 2 -> Taken from 1
........
=>> Treat special parameters
=>> Calc missing parameters
    Processing MM GAS
        Doing 1 MM ELE
    No values for MM_ELE existing -> Skipping
    Processing MM INT
........
=>> Calc delta from raw data
    No data for 0+0 PB ELRAELE 0
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber