here it is. it only generated gb.mdout.
----------------------------------------
Reading parm file (com.prmtop)
title:
UNK
Parameter topology includes 10-12 terms:
These are assumed to be zero here (e.g. from TIP3P water)
mm_options: e_debug=2
mm_options: gb=2
mm_options: rgbmax=25.000000
mm_options: gbsa=0
mm_options: surften=0.007200
mm_options: cut=999.000000
mm_options: epsext=78.300000
mm_options: kappa=0.127315
Processing ASCII trajectory (_MMPBSA_complex.mdcrd.0)
Processing frame 1
iter Total bad vdW elect nonpolar
genBorn frms
eff.c(2717) enb14 --> 1439.428
eff.c(2718) eel14 --> 13044.018
eff.c(2776) enb --> -3091.406
eff.c(2777) eel --> -25645.494
eff.c(2778) e_gb --> nan
eff.c(2779) esurf --> 0.000
eff.c(2780) evdwnp --> 0.000
ff: 0 nan 11474.78 -1651.98 -12601.48 0.00 nan nan
BOND = 3460.1268 ANGLE = 3146.5828 DIHED = 4868.0723
VDWAALS = -3091.4059 EEL = -25645.4944 EGB = nan
1-4 VDW = 1439.4283 1-4 EEL = 13044.0182 RESTRAINT =
0.0000
ESURF = 0.0000
Processing frame 2
eff.c(2717) enb14 --> 1397.678
eff.c(2718) eel14 --> 12973.555
eff.c(2776) enb --> nan
eff.c(2777) eel --> nan
eff.c(2778) e_gb --> -nan
eff.c(2779) esurf --> 0.000
eff.c(2780) evdwnp --> 0.000
BOND = nan ANGLE = 3144.7739 DIHED = 4918.7752
VDWAALS = nan EEL = nan EGB = -nan
1-4 VDW = 1397.6782 1-4 EEL = 12973.5552 RESTRAINT =
0.0000
ESURF = 0.0000
Processing frame 3
eff.c(2717) enb14 --> 1430.030
eff.c(2718) eel14 --> 13018.950
eff.c(2776) enb --> nan
eff.c(2777) eel --> nan
eff.c(2778) e_gb --> -nan
eff.c(2779) esurf --> 0.000
eff.c(2780) evdwnp --> 0.000
BOND = nan ANGLE = 3118.2528 DIHED = 4902.0847
VDWAALS = nan EEL = nan EGB = -nan
1-4 VDW = 1430.0297 1-4 EEL = 13018.9502 RESTRAINT =
0.0000
ESURF = 0.0000
Processing frame 4
eff.c(2717) enb14 --> 1446.811
eff.c(2718) eel14 --> 13107.999
eff.c(2776) enb --> nan
eff.c(2777) eel --> nan
eff.c(2778) e_gb --> -nan
eff.c(2779) esurf --> 0.000
eff.c(2780) evdwnp --> 0.000
BOND = nan ANGLE = 3068.8424 DIHED = 4927.4574
VDWAALS = nan EEL = nan EGB = -nan
1-4 VDW = 1446.8107 1-4 EEL = 13107.9995 RESTRAINT =
0.0000
ESURF = 0.0000
Processing frame 5
eff.c(2717) enb14 --> 1427.264
eff.c(2718) eel14 --> 12980.918
eff.c(2776) enb --> nan
eff.c(2777) eel --> nan
eff.c(2778) e_gb --> -nan
eff.c(2779) esurf --> 0.000
eff.c(2780) evdwnp --> 0.000
BOND = nan ANGLE = 3205.5580 DIHED = 4881.6568
VDWAALS = nan EEL = nan EGB = -nan
1-4 VDW = 1427.2643 1-4 EEL = 12980.9175 RESTRAINT =
0.0000
ESURF = 0.0000
Processing frame 6
eff.c(2717) enb14 --> 1408.232
eff.c(2718) eel14 --> 13076.241
eff.c(2776) enb --> nan
eff.c(2777) eel --> nan
eff.c(2778) e_gb --> -nan
eff.c(2779) esurf --> 0.000
eff.c(2780) evdwnp --> 0.000
BOND = nan ANGLE = 3141.3582 DIHED = 4896.2641
VDWAALS = nan EEL = nan EGB = -nan
1-4 VDW = 1408.2318 1-4 EEL = 13076.2412 RESTRAINT =
0.0000
ESURF = 0.0000
Processing frame 7
eff.c(2717) enb14 --> 1427.465
eff.c(2718) eel14 --> 12985.357
eff.c(2776) enb --> nan
eff.c(2777) eel --> nan
eff.c(2778) e_gb --> -nan
eff.c(2779) esurf --> 0.000
eff.c(2780) evdwnp --> 0.000
BOND = nan ANGLE = 3104.4436 DIHED = 4889.1820
VDWAALS = nan EEL = nan EGB = -nan
1-4 VDW = 1427.4646 1-4 EEL = 12985.3567 RESTRAINT =
0.0000
ESURF = 0.0000
Processing frame 8
eff.c(2717) enb14 --> 1446.095
eff.c(2718) eel14 --> 12976.102
eff.c(2776) enb --> nan
eff.c(2777) eel --> nan
On 02/01/2017 01:37 PM, Vlad Cojocaru wrote:
> This is a PMEMD simulation output and not a PBSA/GBSA output ... I
> thought your problems are with MMPBSA and not with simulations .....
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Received on Wed Feb 01 2017 - 06:30:03 PST
