On 10/01/2020 10:50 PM, aishen wrote:
> Here are my command, I think they aren't right ?
>
> In fact it doesn't do any error but don't produce the expected files ...
>
> sander -O -i mini.in -o mini.out -p dna.prmtop -c dna.rst7 -r mini.rst
> -ref dna.rst7
> sander -O -i heat.in -o heat.out -p dna.prmtop -c mini.rst -r heat.rst
> -x heat.mdcrd -ref mini.rst
> sander -O -i eq.in -o eq.out -p dna.prmtop -c heat.rst -r eq.rst -x
> eq.mdcrd -ref heat.rst
> sander -O -i md.in -o md.out -p dna.prmtop -c eq.rst -r md.rst7 -x md.nc
> -inf mdinfo
>
> and all the files i have in the directory :
>
> A-dna.pdb dna.prmtop dna.rst7 eq.in eq.out heat.in heat.out
> leap.log md.in md.out mini.in mini.out
>
> But it should generate md.rst7 and a md.nc (obviously not created )
according to your e-mail, you issued four isolated sander invokations;
the listing of your files indicates that no rst files have been
produced, which suggests that there is a problem with your first sander
call already.
Thus, have a look into the output of your first call (mini.out); Amber
often yields helpful error messages. Also check your input (formatting,
keywords) and consult the manual, if in doubt.
A look into the other out files may also be instructive to see, how
Amber deals with a non-existent file (coordinate reference is missing in
run 2-4).
Regards,
Anselm
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Received on Fri Oct 02 2020 - 03:30:02 PDT
