Hi,
I want to calculate the binding energy of a monomer in an tetrameric protein
using the MM-PBSA script. So I considered 1 monomer as the ligand and the
other 3 monomers as one receptor.
However, I obtained the following error:
-- > mm_pbsa.pl mm.exp.in > mm.exp.out &
[1] 5572
-- > Use of uninitialized value in concatenation (.) or string at
/warehouse/programs/amber8/amber8_mod//src/mm_pbsa/mm_pbsa_readinput.pm line
76, <IN> line 258.
Use of uninitialized value in string eq at
/warehouse/programs/amber8/amber8_mod//src/mm_pbsa/mm_pbsa_readinput.pm line
164, <IN> line 258.
Use of uninitialized value in string eq at
/warehouse/programs/amber8/amber8_mod//src/mm_pbsa/mm_pbsa_readinput.pm line
164, <IN> line 258.
Use of uninitialized value in string eq at
/warehouse/programs/amber8/amber8_mod//src/mm_pbsa/mm_pbsa_readinput.pm line
164, <IN> line 258.
Use of uninitialized value in string eq at
/warehouse/programs/amber8/amber8_mod//src/mm_pbsa/mm_pbsa_readinput.pm line
164, <IN> line 258.
Use of uninitialized value in exists at
/warehouse/programs/amber8/amber8_mod//src/mm_pbsa/mm_pbsa_readinput.pm line
205, <IN> line 258.
Use of uninitialized value in hash element at
/warehouse/programs/amber8/amber8_mod//src/mm_pbsa/mm_pbsa_readinput.pm line
209, <IN> line 258.
Does anyone knows what this means? Despite this error the calculation ends.
However strangely, I obtain a positive value for the binding energy.
COMPLEX RECEPTOR LIGAND
# ----------------------- -----------------------
-----------------------
# MEAN STD MEAN STD MEAN
STD
# ======================= =======================
=======================
ELE -6192.12 26.99 -4573.36 22.76 -1482.39
12.77
VDW -4702.76 51.11 -3293.75 41.22 -950.18
26.61
INT 21186.50 80.29 15899.56 63.79 5286.94
39.94
GAS 10291.63 86.09 8032.46 70.31 2854.37
46.03
PBSUR 198.18 1.03 169.55 0.90 70.30
0.49
PBCAL 0.00 0.00 0.00 0.00 -1120.46
10.37
PBSOL 198.18 1.03 169.55 0.90 -1050.16
10.20
PBELE -6192.12 26.99 -4573.36 22.76 -2602.86
11.18
PBTOT 10489.80 86.24 8202.01 70.45 1804.21
46.07
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -136.37 6.50
VDW -458.83 9.08
INT -0.00 0.00
GAS -595.20 8.88
PBSUR -41.68 0.35
PBCAL 1120.46 10.37
PBSOL 1078.78 10.41
PBELE 984.09 11.65
PBTOT 483.58 13.27
My script is below. Is there anything wrong with it? Please help me.
PREFIX src
PATH ./
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ./complex.top
RECPT ./complexBCD.top
LIGPT ./complexA.top
#
GC 1
AS 0
DC 0
#
MM 1
GB 0
PB 1
MS 1
#
NM 0
PROC 1
REFE 0
INDI 1.0
EXDI 80.0
SCALE 2.5
LINIT 1000
MAXC 0.001
PRBRAD 1.4
#
FOCUS 0
PERFIL 80.0
CHARGE ./my_amber94_delphi.crg
SIZE ./my_parse_delphi.siz
#
SURFTEN 0.00542
SURFOFF 0.92
#
DIELC 1.0
#
PROBE 0.0
#
BOX NO
NTOTAL 14020
NSTART 3000
NSTOP 5000
NFREQ 50
#
NUMBER_LIG_GROUPS 1
LSTART 1
LSTOP 3505
#
NUMBER_REC_GROUPS 1
RSTART 3506
RSTOP 14020
TRAJECTORY ./md.mdcrd
#
DELPHI /home/delphi/bin/Delphi
Thanks
Jardas
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Received on Wed Jan 31 2007 - 06:07:37 PST
