Hello everyone,
I am trying to get binding energy of a mutated protein with its ligand. After test of mm-pbsa in the Examples, I test it with my own system with mm-pbsa, but always get into trouble and no Bond Vdwaals and 1-4VDW values is given out.
I have check the *prmtop and change different mdcrd to test. But still can not overcome the problem. I have checked the output pdb for the complex when doing pbsa. And the mdcrd is a final 1ns dcd of a 30ns namd dcd file transformed by amber ptraj.
If it is the problem with prmtop, do you have any suggestions on checking it effectively? If not, do you have any suggestions on improving it.
Thanks for your kind help
Pang Xueqin
DICP CAS
The output is as follows:
output of MM-GBSA
#####################################################################################
pro-lig_com.all.out
MM
GB
MS
PB_SURFTEN 0.0072
PB_SURFOFF 0.00
GB_SURFTEN 0.0072
GB_SURFOFF 0.00
1
BOND = 874.7425 ANGLE = 2539.0853 DIHED = 3470.6028
VDWAALS = -2411.0741 EEL = -19336.7814 EGB = -3540.2770
1-4 VDW = 1216.8740 1-4 EEL = 11839.6272 RESTRAINT = 0.0000
surface area = 18310.2767
2
BOND = 10804824.1381 ANGLE = 469191.8854 DIHED = 16271.5596
VDWAALS = ************* EEL = -16973.2372 EGB = -6318.0368
1-4 VDW = ************* 1-4 EEL = 9154.1513 RESTRAINT = 0.0000
surface area = 15517.4713
3
BOND = 13204617.2939 ANGLE = 418026.7166 DIHED = 17233.2463
VDWAALS = ************* EEL = -9439.1589 EGB = -6246.3031
1-4 VDW = ************* 1-4 EEL = 1566.7690 RESTRAINT = 0.0000
surface area = 14823.5458
4
BOND = 14003168.0315 ANGLE = 367093.8707 DIHED = 15489.5072
VDWAALS = 17656579.3728 EEL = -5403.4655 EGB = -6671.6425
1-4 VDW = 12584392.5139 1-4 EEL = -3236.4822 RESTRAINT = 0.0000
surface area = 14913.0201
################################################################################
for ligand
1
BOND = 13.8815 ANGLE = 59.7811 DIHED = 10.7636
VDWAALS = -4.5483 EEL = 57.7862 EGB = -31.8879
1-4 VDW = 14.7125 1-4 EEL = -148.0538 RESTRAINT = 0.0000
surface area = 437.9018
2
BOND = 4168565.8417 ANGLE = 3197.3218 DIHED = 280.5143
VDWAALS = 1947.3745 EEL = 42.7075 EGB = -73.1820
1-4 VDW = 1786.9054 1-4 EEL = -194.0630 RESTRAINT = 0.0000
surface area = 567.2564
3
BOND = 3672258.8967 ANGLE = 5083.0809 DIHED = 268.1229
VDWAALS = 496.5980 EEL = 47.6142 EGB = -103.3002
1-4 VDW = 69893.9067 1-4 EEL = -203.2935 RESTRAINT = 0.0000
surface area = 616.9547
4
BOND = 3525920.4156 ANGLE = 4233.6473 DIHED = 214.1210
VDWAALS = 1701.9453 EEL = 133.8069 EGB = -102.0518
1-4 VDW = 155782.7329 1-4 EEL = -235.6608 RESTRAINT = 0.0000
surface area = 541.3045
##############################################################################################
for receptor, it is almost the same with complex
#################################################################################################
statistics.out
# COMPLEX RECEPTOR LIGAND
# ----------------------- ----------------------- -----------------------
# MEAN STD MEAN STD MEAN STD
# ======================= ======================= =======================
ELE -7957.14 484.44 -7835.75 478.85 -124.79 33.55
VDW 7559347.32 15121083.04 7467306.86 14936935.77 57904.91 73842.80
INT 9830700.17 6680720.34 6985673.57 4917892.95 2845026.60 1916381.89
GAS 17382090.35 19107513.83 14445144.69 18009702.43 2902806.71 1947353.70
GBSUR 114.42 11.82 115.90 12.51 3.89 0.54
GB -5694.06 1447.85 -5714.56 1460.43 -77.61 33.50
GBSOL -5579.65 1459.43 -5598.67 1472.61 -73.71 33.04
GBELE -13651.21 1829.70 -13550.31 1833.17 -202.39 58.12
GBTOT 17376510.70 19106490.92 14439546.02 18008768.64 2902733.00 1947325.44
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE 3.40 28.02
VDW 34135.55 122119.55
INT -0.00 0.00
GAS 34138.95 122099.43
GBSUR -5.38 0.29
GB 98.11 43.39
GBSOL 92.73 43.54
GBELE 101.50 59.65
GBTOT 34231.67 122114.72
###############################################################################################
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
output of pbsa is almost the same with mm-gbsa
input for mm-gbsa
#########################################################################################
# Input parameters for mm_pbsa.pl
#
################################################################################
.GENERAL
#
VERBOSE 0
#
PREFIX E169-A
PATH ./out/.
START 1
STOP 5
OFFSET 1
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ./E169-A.prmtop
RECPT ./E169.prmtop
LIGPT ./A.prmtop
#
GC 0
AS 0
DC 0
#
MM 1
GB 1
PB 0
MS 0
#
NM 0
#
################################################################################
.DECOMP
#
DCTYPE 1
#
COMREC 1-308
COMLIG 309
COMPRI 1-309
RECRES 1-308
RECPRI 1-308
RECMAP 1-308
LIGRES 1
LIGPRI 1
LIGMAP 309
################################################################################
.PB
PROC 2
REFE 0
INDI 1.0
EXDI 78.50
SCALE 2
LINIT 1000
PRBRAD 1.4
ISTRNG 0.0
RADIOPT 0
NPOPT 1
#
SURFTEN 0.0072
SURFOFF 0.00
#
IVCAP 0
CUTCAP -1.0
XCAP 0.0
YCAP 0.0
ZCAP 0.0
#
################################################################################
.MM
DIELC 1.0
#
################################################################################
.GB
IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 78.50
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
################################################################################
.MS
PROBE 0.0
#
#################################################################################
.NM
DIELC 4
MAXCYC 10000
DRMS 0.0001
#
#################################################################################
.MAKECRD
NTOTAL 134833
NSTART 1
NSTOP 5
NFREQ 1
NUMBER_LIG_GROUPS 1
LSTART 4882
LSTOP 4921
NUMBER_REC_GROUPS 1
RSTART 1
RSTOP 4881
#
#################################################################################
TRAJECTORY E169-A-f5.mdcrd
############################################################################################
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
input of mm-pbsa
the following is changed in pbsa-input
#
GC 1
AS 0
DC 0
#
MM 1
GB 1
PB 1
MS 1
#
NM 0
#
################################################################################
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Received on Thu Jan 14 2010 - 08:00:02 PST
