AMBER Archive (2006)

Subject: AMBER: strange mm_pbsa output

From: alfredoq_at_fcq.unc.edu.ar
Date: Sat May 13 2006 - 10:44:58 CDT

Dear Amber community,

I applyed the mm_pbsa.pl script to determine the binding free energy o a ligand
to a protein. My statistics.out file shows the following:

# COMPLEX RECEPTOR LIGAND
# ----------------------- -----------------------
-----------------------
# MEAN STD MEAN STD MEAN
STD
# ======================= =======================
=======================
ELE -5303.15 5519.36 -5155.80 5535.87 -136.49
54.45
VDW -2632.54 0.00 -2602.06 0.00 3789742.36
12298842.54
INT 49573990.99 8657606.35 49456164.03 8679472.59 117868.77
287132.38
GAS 49566055.30 8658148.78 49448406.17 8679936.88 3907474.64
12302734.61
PBSUR 169.35 8.90 169.16 8.64 2.75
0.29
PBCAL -15530.45 2187.51 -15500.38 2171.48 -65.88
23.29
PBSOL -15361.11 2187.01 -15331.21 2171.10 -63.13
23.22
PBELE -20833.60 5366.67 -20656.18 5341.50 -202.37
54.81
PBTOT 49550694.19 8657701.57 49433074.95 8679489.35 3907411.51
12302734.03
GBSUR 243.86 12.82 243.60 12.44 3.96
0.41
GB -17701.21 1411.59 -17683.36 1406.15 -69.60
26.15
GBSOL -17457.35 1405.56 -17439.76 1400.41 -65.64
26.06
GBELE -23004.36 5678.48 -22839.16 5681.10 -206.09
55.32
GBTOT 49548597.95 8657432.67 49430966.41 8679215.96 3907408.99
12302735.31

# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -10.86 79.84
VDW -3789772.84 12298842.54
INT -41.81 373.08
GAS -3789825.50 12298813.02
PBSUR -2.57 0.78
PBCAL 35.80 213.86
PBSOL 33.24 213.81
PBELE 24.95 222.28
PBTOT -3789792.27 12298821.27
GBSUR -3.70 1.12
GB 51.75 50.11
GBSOL 48.06 49.49
GBELE 40.90 78.04
GBTOT -3789777.45 12298812.93

Analyzing these results I was very stranged by the quite large values of the VDW
and GAS components and the corresponding SD. During the calculation the
following warning messages appeared:

vertex atom mismatch
       atom: 1398
vertex atom: 1395
molsurf: molsurf.c:1055: is_buried: Assertion `sarg1 >= 0.0' failed.
vertex atom mismatch
       atom: 2429
vertex atom: 2428
vertex atom mismatch
       atom: 2798
vertex atom: 2795
vertex atom mismatch
       atom: 2998
vertex atom: 2995
vertex atom mismatch
       atom: 3098
vertex atom: 3095
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment
No skew or curtosis when zero variance in moment

I run the MD simulation in explicit solvent, and I stripped the waters and
counter ion previous to the mm_pbsa analysis. I also created new prmtop files
of the complex, the receptor and ligand without waters for mm_pbsa.
Any hint about what's going wrong with my system or why these large values
appears would be greatly appreciated,
Thanks

Alfredo Quevedo
Facultad de Ciencias Químicas
Universidad Nacional de Córdoba
Argentina

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