I don't know if you got the exactly same error with me but I had the same
problem this morning. If you are preparing min.in file in windows10
directly, sander is refusing your min.in file. Just run
windows10-ubuntu-bash and prepare this file with vi-editor and save it with
":wq" command (I solved my problem with this way I hope it will help you
too).
David A Case <david.case.rutgers.edu>, 27 Şub 2019 Çar, 22:10 tarihinde
şunu yazdı:
> On Tue, Feb 26, 2019, Sasthi Charan Mandal wrote:
>
> >It shows only syntax error.
> >
> >On Tue, Feb 26, 2019 at 11:12 PM Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> >> What is the exact error message you receive?
> >>
> >> > I am following the simulation of small fragment of DNA from
> >> > ambertools tutorial. But I stuck on energy minimization step. the
> >> > command : $AMBERHOME/bin/sander
> >> > -O -i polyAT_vac_init_min.in -o polyAT_vac_init_min.out -c
> >> polyAT_vac.rst7
> >> > -p polyAT_vac.prmtop -r polyAT_vac_init_min.ncrst is not working and
> it
> >> > shows syntax error. Do I have to modify the command? could you please
> >> help
>
> We really need *exact* details, with a very strict interpretation of
> the word "exact".
>
> Did you type by hand the above command at the shell prompt? Was
> everything on a single line? Can you copy and paste both what you typed
> and the entire response that came to the terminal? Is there anything in
> the " polyAT_vac_init_min.out" file?
>
> ....dac
>
>
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Received on Wed Feb 27 2019 - 14:00:03 PST
