On Wed, Jun 5, 2013 at 2:59 PM, Rasha Alqus <rasha.alqus.manchester.ac.uk>wrote:
>
>
> Dear Amber users,
>
>
>
> I would like to perform energy minimization of compound in water, first
> with restrain on mu compound only which is formed from 4260 atom, when i
> submitted a job i get an error in the file attached. Can any one help me to
> solve it
>
>
>
> Regards
>
> rasha
>
>
>
> the minimization input file contain:
>
>
>
> initial minimization prior to MD with restrain on x
>
> &cntrl
>
> imin=1,
>
> maxcyc=2000,
>
> ncyc=500,
>
> ntb=0,
>
If your system is solvated, I'm guessing you want ntb=1 (periodic boundary
conditions).
>
>
>
> ntr=1,
>
>
>
> ntpr=10,
>
>
>
> cut=12
>
If ntb==1 (which it almost always is for simulations with explicit
solvent), then I suggest reducing the cutoff to somewhere between 8 and 10
Å. If ntb==0, you should select a GB model (unless you want to simulate in
vacuum??) and set cut much larger.
However, the error message in the attached file suggests that the shell
was trying to parse "-i" as a command, which probably means that you are
not running sander correctly.
Check the script file and make sure that all of the command-line flags are
on the same line as the sander command (they appear not to be). If you
want to split a command up into multiple lines, you must end each line with
a forward-slash (\) to indicate to the shell that the line should be
continued.
There must be no spaces after the \ at the end of the line. Also, if you
are creating the file with dos-line endings (because you are editing the
file in some Windows text editor), then the dos carriage returns may be
causing issues, too. (Some Mac editors have the same problem, I think).
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Jun 05 2013 - 12:30:16 PDT
