Dear Amber Users,
I have the following problem.
I performed MD simulation with NAMD2.6 on a GPCR/ligand complex in
membrane bilayer environement (ff03 for GPCR, TIP3P water model, GAFF
for ligand and POPC - prepared with AMBER8 antechamber and tleap).
I would like to perform MM-PBSA calculation on the GPCR/ligand complex.
In the first step only the heating process was analysed (the *.dcd file
was converted into *.mdcrd by means of the ptraj modeule of AMber9),
because it contains only 64 frame.
The config files are attached (01_EXTRACT_COOR.IN, 02_MMPBSA.IN)
The obtained coordinates were checked and were correct, but in the
calculated values we obtained interesting results.
The DGbind(INT) was not equal to zero, and the calculated DGbind was
high due to the high vdW values (03_cH4R_proton_heat_statistics).
In the last 2 ns of the production run only the MM part was extracted
and in cases of INT and VDW we obtained the same behavior
(04_H4complex_equil_norst8_statistics.out).
Are the scripts correct, or there is typo in my scripts. Unfortunately
I've no permession to send the coordinate files.
Thank you for your help in advance.
Balazs Jojart
.GENERAL
PREFIX cH4R_proton_heat
PATH ./
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT ./complex.parm7 ==> OBTAINED FROM THE INITIAL COORDINATES OF GPCR/LIGAND SYSTEM
RECPT ./H4R.parm7 ==> OBTAINED FROM THE INITIAL COORDINATES OF THE RECEPTOR
LIGPT ./HRL.parm7 ==> OBTAINED FROM THE INITIAL COORDINATES OF THE LIGAND
GC 1
AS 0
DC 0
MM 0
GB 0
PB 0
MS 0
NM 0
.MAKECRD
BOX YES
NTOTAL 67515
NSTART 1
NSTOP 1314
NFREQ 1
NUMBER_LIG_GROUPS 1
LSTART 4656
LSTOP 4673
NUMBER_REC_GROUPS 1
RSTART 1
RSTOP 4655
.TRAJECTORY
TRAJECTORY ./H4complex_heat.mdcrd
.PROGRAMS
.GENERAL
PREFIX cH4R_proton_heat
PATH ./
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT ./complex.parm7
RECPT ./H4R.parm7
LIGPT ./HRL.parm7
GC 0
AS 0
DC 0
MM 1
GB 1
PB 1
MS 1
NM 0
.PB
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
.MM
DIELC 1.0
.GB
IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
SURFTEN 0.0072
SURFOFF 0.00
.MS
PROBE 0.0
.PROGRAMS
# COMPLEX RECEPTOR LIGAND
# ----------------------- ----------------------- -----------------------
# MEAN STD MEAN STD MEAN STD
# ======================= ======================= =======================
ELE -3208.78 34.37 -3160.22 35.24 29.54 0.69
VDW -755.46 135.91 -1418.83 118.02 0.19 0.33
INT 4874.43 1015.35 4850.42 1011.43 27.86 3.72
GAS 910.19 1113.78 271.37 1097.06 57.59 3.44
PBSUR 105.72 0.39 106.47 0.39 2.17 0.00
PBCAL -3555.51 22.31 -3569.12 22.16 -71.76 0.54
PBSOL -3449.79 22.21 -3462.65 22.11 -69.58 0.54
PBELE -6764.29 25.64 -6729.34 25.42 -42.22 0.40
PBTOT -2539.60 1122.37 -3191.28 1107.86 -12.00 3.59
GBSUR 105.72 0.39 106.47 0.39 2.17 0.00
GB -3905.40 24.20 -3916.92 26.00 -70.86 0.57
GBSOL -3799.67 24.34 -3810.45 26.16 -68.69 0.57
GBELE -7114.18 12.31 -7077.14 11.60 -41.33 0.46
GBTOT -2889.48 1136.06 -3539.08 1121.82 -11.10 3.74
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -78.10 5.54
VDW 663.18 54.03
INT -3.85 1.26
GAS 581.23 51.51
PBSUR -2.91 0.02
PBCAL 85.36 3.07
PBSOL 82.45 3.08
PBELE 7.26 2.97
PBTOT 663.68 52.47
GBSUR -2.91 0.02
GB 82.38 4.26
GBSOL 79.47 4.28
GBELE 4.29 2.20
GBTOT 660.70 53.15
# COMPLEX RECEPTOR LIGAND
# ----------------------- ----------------------- -----------------------
# MEAN STD MEAN STD MEAN STD
# ======================= ======================= =======================
ELE -3986.06 47.21 -3945.99 46.58 30.14 1.63
VDW -272.70 215.77 -1069.12 25.66 0.06 0.53
INT 6396.38 50.07 6367.67 49.90 34.20 2.98
GAS 2137.62 223.10 1352.55 64.00 64.40 3.18
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -70.20 7.19
VDW 796.36 213.39
INT -5.49 1.27
GAS 720.66 213.21
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Received on Sun Jul 01 2007 - 06:07:53 PDT
