That's right, I created the box by solvating the molecule and it worked.
Thank you:)
Can you tell me how else I can set for the mol? I could do that only by
solvating the mol.
Thanks again for the help.
On Wed, Jul 22, 2015 at 2:22 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Since you didn't post what input you used I can only guess, but it seems
> like you are specifying periodic boundary conditions (ntb > 0) but your
> coordinates have no box information. Either set ntb to 0 or add a box.
>
> -Dan
>
> On Tue, Jul 21, 2015 at 3:29 PM, Mohsen Zakeri <mohsen.zakery.gmail.com>
> wrote:
>
> > Hi,
> >
> > I am trying to run a minimization for a protein-ligand complex using
> > sander. I produce the "prmtop" and "inpcrd" files with leap program for
> the
> > pdb file. but when I try to run the sander minimization command I get the
> > following line in the "min.out" as an error:
> > "peek_ewald_inpcrd: Box info not found in inpcrd".
> > Can any body help me with this error?
> >
> >
> > *The sander command I used is this:*
> > sander -O -i min.in -o min.out -p pl.prmtop -c pl.inpcrd -r min.rst
> -inf
> > min.mdinfo
> >
> > *The "min.out" looks like this:*
> >
> >
> --------------------------------------------------------------------------------
> > 1. RESOURCE USE:
> >
> >
> --------------------------------------------------------------------------------
> >
> > |
> > Flags:
> >
> > getting new box info from bottom of inpcrd
> > | INFO: Old style inpcrd file read
> >
> > | peek_ewald_inpcrd: Box info not found in inpcrd
> >
> >
> > I really appreciate your help:)
> > Thanks.
> >
> > Sincerely,
> > -Mohsen
> >
> > --
> > Mohsen Zakeri, B.Sc.
> > ECE Department, Computer Engineering
> > University of Tehran, Tehran, Iran
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Mohsen Zakeri, B.Sc.
ECE Department, Computer Engineering
University of Tehran, Tehran, Iran
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Received on Tue Jul 21 2015 - 15:30:02 PDT
