Thanks, I will read them more:)
On Jul 22, 2015 2:54 AM, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
> 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)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Jul 21 2015 - 15:30:04 PDT
