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.uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================
-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf
Of musa özboyacı
Sent: Thursday, January 22, 2009 9:07 AM
To: AMBER.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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Received on Fri Jan 23 2009 - 01:23:00 PST
