yes it worked
thank you
On Wed, May 15, 2019 at 7:33 PM Pratul Agarwal <pratul.agarwal-lab.org>
wrote:
> Looking again, there does seem to be something missing.
>
> Can you try repeat the step with "-c wt1mg_min.rst" instead of
> wt1mg_min_water.rst?
>
> Pratul K. Agarwal, Ph.D.
> (Editorial Board Member: PLoS ONE, Microbial Cell Factories)
> Web: http://www.agarwal-lab.org/
>
>
> On 5/15/2019 2:12 PM, Pratul Agarwal wrote:
>
> Try this before running sander
>
>
> cp wt1mg.crd wt1mg.rst
>
>
>
> See the text below from the previous step of the tutorial.
> http://ambermd.org/tutorials/advanced/tutorial8/loop5.htm
>
> "Notice the "-ref" option at the end of the command line. This option is
> normally not required. In this case, we need to have it because we are
> doing a restrained minimization and this information is required for sander
> to be able to map the residue selections we specified in our "min.in".
> The file "wt1mg.rst" is the same file as the original restart file we
> generated at the end of tleap preparation. Simply copy the original file
> wt1mg.crd into wt1mg.rst. (The reason we make another copy of the same file
> is only for bookkeeping. You can use the same wt1mg.crd if you want.) "
>
>
> Pratul K. Agarwal, Ph.D.
> (Editorial Board Member: PLoS ONE, Microbial Cell Factories)
> Web: http://www.agarwal-lab.org/
>
>
> On 5/15/2019 2:06 PM, Sadaf Rani wrote:
>
> Hi Amber users
> I am following the tutorial
> http://ambermd.org/tutorials/advanced/tutorial8/loop6.htm and when it
> reaches at the step mentioned in link it ask for a file to use with -c
> flag wt1mg_min_water.rst
> however in previous steps no such file is generated; the previous command
> is:-
> sander -O -i min.in -p wt1mg.parm7 -c wt1mg.crd -r wt1mg_min.rst -o
> wt1mg_min_water.out -ref wt1mg.rst
> It generates wt1mg.rst as the restart file, and wt1mg_min_water.out as the
> output file. What about the wt1mg_min_water.rst file?
> I am getting confused here
> Please suggest me
> Thank you
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Received on Tue May 28 2019 - 02:30:02 PDT
