Dear Jason,
I didn't change the topology file at all, only the input coordinate file
(and only to add the size of the box at the bottom). Will this cause
problems? The minimization in sander seemed to proceed without problems,
but I'm not sure. The solvent box is a cube, and I am minimizing under no
pressure regulation (ntp = 0)
Best,
Brandon
On Thu, Jun 21, 2012 at 11:48 AM, Jason Swails <jason.swails.gmail.com>wrote:
> Some possible pitfalls to be aware of here: Some tasks require certain
> settings in the topology file in order to operate properly. For instance,
> the IFBOX pointer determines the imaging that's done, if any (is the box
> orthogonal or not?), and the SOLVENT_POINTERS and ATOMS_PER_MOLECULE
> section are only added in LEaP if a periodic box is defined, and these
> sections are used, I believe, for both constant pressure and wrapping.
>
> You should check your topology file for the appropriate properties, or
> re-make the topology file using "setbox" in LEaP, if you are suspicious of
> possible problems.
>
> HTH,
> Jason
>
> On Thu, Jun 21, 2012 at 11:37 AM, Brandon Sim <simpavid.gmail.com> wrote:
>
> > Thanks! For future reference, I added the sidelength of the cubic box
> three
> > times in a separate line at the bottom of the inpcrd file manually, and
> > this worked.
> >
> > Best,
> > Brandon
> >
> > On Thu, Jun 21, 2012 at 9:47 AM, Jason Swails <jason.swails.gmail.com
> > >wrote:
> >
> > > Look at the "setbox" command in LEaP. This will add the proper box
> > > information to both the inpcrd file and the topology file to enable
> > > periodic boundary simulations.
> > >
> > > HTH,
> > > Jason
> > >
> > > On Thu, Jun 21, 2012 at 8:31 AM, Brandon Sim <simpavid.gmail.com>
> wrote:
> > >
> > > > Dear all,
> > > >
> > > > I am attempting to use sander for minimization of structures, but the
> > > > following error occurs:
> > > >
> > > > getting new box info from bottom of inpcrd
> > > > | INFO: Old style inpcrd file read
> > > > | peek_ewald_inpcrd: Box info not found in inpcrd
> > > >
> > > > I am wondering if there is a way to manually add this information to
> > the
> > > > end of the inpcrd file if I know the dimensions of my solvent box. I
> > ask
> > > if
> > > > there is a manual solution because I did not use leap to add solvent;
> > > > instead, I used the MMTSB toolset.
> > > >
> > > > Thanks,
> > > > Brandon
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Candidate
> > > 352-392-4032
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 21 2012 - 11:00:03 PDT
