AMBER Archive (2007)

Subject: AMBER: mm_pbsa_statistics.pl

From: Antonio Morreale (amorreale_at_cbm.uam.es)
Date: Tue Jan 16 2007 - 06:28:52 CST


Hi,

Please, find bellow the result of running mm_pbsa_statistics.pl:

=>> 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. snaps_com.all.out: -
    2. snaps_rec.all.out: -
    3. snaps_lig.all.out: -
=>> Reading files
    Reading snaps_com.all.out
    WARNING: Missing SURF for MS in 0 -> Taken from -1
    WARNING: Missing SURF for MS in 11 -> Taken from 10
    WARNING: Missing SURF for MS in 18 -> Taken from 17
    WARNING: Missing SURF for MS in 56 -> Taken from 55
    WARNING: Missing SURF for MS in 69 -> Taken from 68
    WARNING: Missing SURF for MS in 102 -> Taken from 101
    WARNING: Missing SURF for MS in 104 -> Taken from 103
    WARNING: Missing SURF for MS in 112 -> Taken from 111
    WARNING: Missing SURF for MS in 154 -> Taken from 153
    Reading snaps_rec.all.out
    Checking CALC
    WARNING: Missing SURF for MS in 0 -> Taken from -1
    WARNING: Missing SURF for MS in 112 -> Taken from 111
    WARNING: Missing SURF for MS in 145 -> Taken from 144
    WARNING: Missing SURF for MS in 154 -> Taken from 153
    WARNING: Missing SURF for MS in 161 -> Taken from 160
    Reading snaps_lig.all.out
    Checking CALC
=>> Treat special parameters
Use of uninitialized value in multiplication (*) at /data/ortizg/software/Linux/amber8/src/mm_pbsa/mm_pbsa_statistics.pm line 1368.
Use of uninitialized value in multiplication (*) at /data/ortizg/software/Linux/amber8/src/mm_pbsa/mm_pbsa_statistics.pm line 1368.
=>> Calc missing parameters
    Processing MM GAS
        Doing 1 MM ELE
    No values for MM_ELE existing -> Skipping
    Processing MM INT
        Doing 1 MM BOND
        Doing 1 MM ANGLE
        Doing 1 MM DIHED
        Doing 1 MM BOND
        Doing 1 MM ANGLE
        Doing 1 MM DIHED
        Doing 1 MM BOND
        Doing 1 MM ANGLE
        Doing 1 MM DIHED
    Processing MM ELE
        Doing 1 MM ELENB
        Doing 1 MM ELE14
        Doing 1 MM ELENB
        Doing 1 MM ELE14
        Doing 1 MM ELENB
        Doing 1 MM ELE14
    Processing MM VDW
        Doing 1 MM VDWNB
        Doing 1 MM VDW14
        Doing 1 MM VDWNB
        Doing 1 MM VDW14
        Doing 1 MM VDWNB
        Doing 1 MM VDW14
    Processing GB GBTOT
        Doing 1 GB GBSOL
    No values for GB_GBSOL existing -> Skipping
    Processing GB GBELE
        Doing 1 GB GB
        Doing 1 MM ELE
        Doing 1 GB GB
        Doing 1 MM ELE
        Doing 1 GB GB
        Doing 1 MM ELE
    Processing GB GBSOL
        Doing 1 GB GB
        Doing 1 GB GBSUR
        Doing 1 GB GB
        Doing 1 GB GBSUR
        Doing 1 GB GB
        Doing 1 GB GBSUR
    Processing MM GAS
        Doing 1 MM ELE
        Doing 1 MM VDW
        Doing 1 MM INT
        Doing 1 MM ELE
        Doing 1 MM VDW
        Doing 1 MM INT
        Doing 1 MM ELE
        Doing 1 MM VDW
        Doing 1 MM INT
    Processing GB GBTOT
        Doing 1 GB GBSOL
        Doing 1 MM GAS
        Doing 1 GB GBSOL
        Doing 1 MM GAS
        Doing 1 GB GBSOL
        Doing 1 MM GAS
=>> Calc delta from raw data
    No data for 0+0 MS SURF 0

I know that warning are because of missing MS values, but, what about
No data for 0+0 MS SURF 0?

Any hint will be valuable?

Best regards.
Antonio

--
Antonio Morreale
Unidad de Bioinformática
Centro de Biologia Molecular "Severo Ochoa"
Universidad Autonoma de Madrid
Cantoblanco, 28049 Madrid (Spain)
Phone: (34) 91-497-2377
Fax:   (34) 91-397-4799
e-mail: amorreale_at_cbm.uam.es
web: http://ub.cbm.uam.es/

----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu