AMBER Archive (2009)

Subject: RE: [AMBER] MM - PBSA problem

From: Ray Luo (rayhuangluo_at_gmail.com)
Date: Thu Jan 22 2009 - 11:31:53 CST

Dear Musa,

Could you be more specific on which distribution of Amber you are using?
What's your input file?

All the best,
Ray

==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo_at_uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf
Of musa özboyacı
Sent: Thursday, January 22, 2009 9:07 AM
To: AMBER_at_ambermd.org
Subject: [AMBER] MM - PBSA problem

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
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