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 Wed May 15 2019 - 12:00:02 PDT
