AMBER Archive (2003)

Subject: AMBER: nmode statistics

From: kbyun_at_wesleyan.edu
Date: Wed Dec 17 2003 - 13:52:51 CST

Hi,
I ran nmode for my protein-RNA system for the complex,
ligand, and receptor for 3 snapshots. I do get the
outputs in the files file_com.all.out, file_lig.all.out,
and file_rec.all.out. I don't get the file that
contains the statistics for the results
file_statistics.out .

The error message given is listed below. How can I get
the statistics and what is wrong with my nmode run?

Thanks,

Suzie Byun

=>> Doing statistics
=>> 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. u1arna_wtup_com.all.out: -
    2. u1arna_wtup_rec.all.out: -
    3. u1arna_wtup_lig.all.out: -
=>> Reading files
    Reading u1arna_wtup_com.all.out
    WARNING: Missing SVIB for NM in 0 -> Taken from -1
    WARNING: Missing STOT for NM in 0 -> Taken from -1
    WARNING: Missing SVIB for NM in 1 -> Taken from 0
    WARNING: Missing STOT for NM in 1 -> Taken from 0
    Reading u1arna_wtup_rec.all.out
    Checking CALC
    Reading u1arna_wtup_lig.all.out
    Checking CALC
    WARNING: Missing SVIB for NM in 0 -> Taken from -1
    WARNING: Missing STOT for NM in 0 -> Taken from -1
    WARNING: Missing SVIB for NM in 2 -> Taken from 1
    WARNING: Missing STOT for NM in 2 -> Taken from 1
=>> Treat special parameters
Use of uninitialized value in multiplication (*) at
/usr/apps/chemistry/Amber/amber7.2/src/mm_pbsa/mm_pbsa_statistics.pm
l
ine 1258.
Use of uninitialized value in multiplication (*) at
/usr/apps/chemistry/Amber/amber7.2/src/mm_pbsa/mm_pbsa_statistics.pm
l
ine 1258.
Use of uninitialized value in multiplication (*) at
/usr/apps/chemistry/Amber/amber7.2/src/mm_pbsa/mm_pbsa_statistics.pm
l
ine 1258.
Use of uninitialized value in multiplication (*) at
/usr/apps/chemistry/Amber/amber7.2/src/mm_pbsa/mm_pbsa_statistics.pm
l
ine 1258.
Use of uninitialized value in multiplication (*) at
/usr/apps/chemistry/Amber/amber7.2/src/mm_pbsa/mm_pbsa_statistics.pm
l
ine 1258.
Use of uninitialized value in multiplication (*) at
/usr/apps/chemistry/Amber/amber7.2/src/mm_pbsa/mm_pbsa_statistics.pm
l
ine 1258.
=>> Calc missing parameters
=>> Calc delta
    No data for 0+0 NM SVIB 0

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