You may find some of the introductory Amber tutorials useful:
http://ambermd.org/tutorials/#basic_tut
On Tue, Jul 21, 2015 at 4:08 PM, Mohsen Zakeri <mohsen.zakery.gmail.com>
wrote:
> 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)
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> 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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Received on Tue Jul 21 2015 - 15:30:03 PDT
