Hi,
This is not a bug. You need to pay attention to the warnings cpptraj
is giving you:
On Tue, Oct 18, 2016 at 7:56 AM, MOHD HOMAIDUR RAHMAN
<rahmanhpu.gmail.com> wrote:
> GB/SA calculation is performed only when* igb>0*
You are trying to perform a GB energy calculation on a periodic
system. If you do not specify input options for 'esander' cpptraj will
try to choose appropriate defaults; this is what the warnings are
about:
> Warning: 'ntb' not specified; setting to 1 based on box type 'Orthogonal'
> Warning: 'cut' not specified; setting to 8.0 based on 'ntb'
So because you didn't tell it otherwise, cpptraj chose defaults based
on the fact that the system has unit cell parameters. The sander
backend will not let you specify gbsa > 0 for a periodic calculation
and tells you so:
> GB/SA calculation is performed only when* igb>0*
> Warning: Action [esander] failed, frame 0.
You should provide the correct input to the 'esander' command (e.g.
ntb 0 igb 1 cut 9999 etc).
-Dan
> 0% 10% 20% 31% 41% 51% 61% 71% 82% 92% 100% Complete.
>
> Thanks & regards
>
> Rahman
>
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-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue Oct 18 2016 - 06:00:03 PDT
