Hi, all,
When I calculate the binding energy of RNA-small molecule interaction by MM_PBSA in AMBER9. Input file is as following:
PREFIX snapshot
PATH ./
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ./1y26_a.prmtop
RECPT ./1y26.prmtop
LIGPT ./a.prmtop
#
GC 0
AS 0
DC 0
#
MM 1
GB 1
PB 1
MS 1
#
NM 0
#
#
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 2
LINIT 1000
PRBRAD 1.4
ISTRNG 0.0
RADIOPT 0
NPOPT 1
CAVITY_SURFTEN 0.0072
CAVITY_OFFSET 0.00
#
SURFTEN 0.0072
SURFOFF 0.00
#
IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
when I run the mm_pbsa.pl, it shows
Use of uninitialized value in multiplication (*) at /export/home/gz/soft/amber9/src/mm_pbsa/mm_pbsa_statistics.pm line 1336.
Use of uninitialized value in multiplication (*) at /export/home/gz/soft/amber9/src/mm_pbsa/mm_pbsa_statistics.pm line 1336.
No data for 0+2 PB PB 0
the output file are like this :
MM
GB
PB
MS
1
BOND = 617.4072 ANGLE = 1269.1704 DIHED = 1818.2919
VDWAALS = -1366.1237 EEL = 32178.2971 EGB = -41925.7449
1-4 VDW = 639.5718 1-4 EEL = -6010.0127 RESTRAINT = 0.0000
corrected reaction field energy: -71281.229816
surface area = 12031.916
ECAVITY = 12031.916
EDISPER = 0.0000
2
BOND = 579.3947 ANGLE = 1293.0841 DIHED = 1823.4181
VDWAALS = -1342.5240 EEL = 32086.1669 EGB = -41862.3644
1-4 VDW = 644.4107 1-4 EEL = -5959.7021 RESTRAINT = 0.0000
corrected reaction field energy: -71145.860423
surface area = 12105.554
ECAVITY = 12105.554
EDISPER = 0.0000
there are no statistics file
How can I fix this ?
Thank you
2010-04-16
Zhou Gong
School of Physics
Huazhong University of Science and Technology
Wuhan
Hubei Province
China
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Received on Fri Apr 16 2010 - 06:30:02 PDT
