On Mon, 2015-07-27 at 11:54 +0200, Albert wrote:
> Hello:
>
> I've calculated MM/PBSA with following parameters:
>
> Input file for running PB & GB
> &general
> endframe=400, verbose=0, interval=4
> /
> &pb
> fillratio=4.0, istrng=0,
> inp = 1, radiopt = 0, indi = 4.0,
> /
>
> However, I notice that the results are strange:
>
>
> Differences (Complex - Receptor - Ligand):
> Energy Component Average Std. Dev. Std. Err.
> of Mean
> -------------------------------------------------------------------------------
> VDWAALS -31.3401 2.3224 0.2322
> EEL -8.2072 0.7814 0.0781
> EPB 8.9154 0.6810 0.0681
> ENPOLAR -2.7111 0.0617 0.0062
> EDISPER 0.0000 0.0000 0.0000
>
> DELTA G gas 0.0000 0.0000 0.0000
> DELTA G solv 0.0000 0.0000 0.0000
>
> DELTA TOTAL 0.0000 0.0000 0.0000
>
> -------------------------------------------------------------------------------
> -------------------------------------------------------------------------------
>
> Does anybody have any idea?
I can reproduce this issue using the test case. The problem appears to
be that the last three items are not computed properly when verbose=0 is
set. If you remove the "verbose" flag from the input file, this issue
should go away.
I will look into a fix.
Thanks for the report,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jul 27 2015 - 07:00:03 PDT
