AMBER: output of mm_pbsa.log

From: Xiao He <hx.itcc.nju.edu.cn>
Date: Sat, 25 Sep 2004 17:30:16 +0800

Dear Amber users,

Output of mm_pbsa.log:
    Processing MM GAS
        Doing 1 MM ELE
        Doing 1 MM VDW
    No values for MM_VDW 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 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

..........

What does these warnings mean?
    No values for MM_VDW existing -> Skipping
    No values for GB_GBSOL existing -> Skipping

and in my previous e-mail the rmsd is very big
# MEAN STD
# =======================
ELE -11.64 2.64
VDW -47.10 1.67
INT 0.71 0.48
GAS -58.03 2.81
PBSUR -4.62 0.07
PBCAL -555.26 284.58
PBSOL -559.88 284.55
PBELE -566.90 286.01
PBTOT -617.91 285.92
GBSUR -6.65 0.10
GB 30.25 2.95
GBSOL 23.60 3.00
GBELE 18.60 1.13
GBTOT -34.43 1.69

Dose that mean it has not been the equivalent state?

Thanks in advance!

        Xiao He
        hx.itcc.nju.edu.cn
          2004-09-25



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Received on Sat Sep 25 2004 - 10:53:00 PDT
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