Lots of "nan" for different energy terms .... hard to say exactly what,
but something looks very wrong with your system .... Do you have anybody
at your site (colleague, supervisor) that can help with this ? It looks
to me like you need a detailed troubleshooting which is hard to do over
email ....
I could think of different things:
1. Can you run exactly your MMPBSA setup on top/crd files provided with
the Amber tests .... (just go the test dir, search for MMGBSA tests and
try to run the test but with your own scripts). If this does not work,
there is something wrong in your running; if this works, the problem may
be in your topology file ....
2. Can properly visualize your topologies with the trajectories in VMD
or other visualization software ?
3. Do every step in the MMPBSA separately and identify where in the
workflow the first problems appear
Best
Vlad
On 02/01/2017 03:18 PM, Albert wrote:
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Vlad Cojocaru, Ph.D., Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Wed Feb 01 2017 - 07:00:02 PST
