Another tip is to use "netcdf=1" in the &general section. This will tell
you immediately if there is a mismatch in your trajectory and topology
files (which is what I suspect given the NaNs).
HTH,
Jason
On Wed, Feb 1, 2017 at 9:35 AM, Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> 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 .....
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
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Received on Wed Feb 08 2017 - 21:30:03 PST
