Hi
I still have problem with the rst file!
When I want to make a pdb file -->Error: Could not read restart atoms/time.
Is there anyway to change the format to default one?!
And I attached the minimization output.I couldn't find a way for it!
$ /opt/amber16/bin/sander -O -i EGFR07_wat_min3.in -o EGFR07_wat_min3.out -p EGFR07-wat.prmtop -c EGFR07_wat_min2.rst -r EGFR07_wat_min3.rst -ref EGFR07_wat_min2.rst
Best Regards
On Mon, 12/19/2016 11:41 AM, Nhai <nhai.qn.gmail.com> wrote:
> Please look at top 4 posts in google results for
>
> "rfree end of unit 5 amber"
>
> Let us know if you still get the trouble.
>
> Ps: you did not see netcdf format because you always use the default format. And like I said, amber16 changes its default format.
>
> Hai
>
> > On Dec 19, 2016, at 11:26 AM, Mohaddeseh Habibzadeh " target="_blank"><m.habibzadeh.azaruniv.edu> wrote:
> >
> > Really?
> > I didn't see this format before when I used amber14.
> > I have 3 consecutive minimizations, for the last one it terminated abnormally without any rst file, because of this I thought that the "min2.rst" file caused this.
> > What is the reason of this ending in "min3.out" --> rfree: End of file on unit 5
> > Thank you very much
> >
> >> On Mon, 12/19/2016 11:11 AM, Nhai " target="_blank"><nhai.qn.gmail.com> wrote:
> >> It's normal. Amber16 uses netcdf format as default.
> >>
> >> Hai
> >>
> >>> On Dec 19, 2016, at 10:54 AM, Mohaddeseh Habibzadeh " target="_blank">" target="_blank"><m.habibzadeh.azaruniv.edu> wrote:
> >>>
> >>> Hello every one
> >>> I'm using amber16. When minimizing, the restart file is not normal as you can see in the attachment.
> >>> I couldn't find out where's the problem!
> >>> Would you please tell me what I have to do?
> >>> Regards
> >>> <Screenshot from 2016-12-19 19:24:27.png>
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Received on Tue Dec 20 2016 - 01:00:02 PST
