On Tue, Mar 26, 2013 at 10:38 AM, Ignacio J. General <ijgeneral.gmail.com>wrote:
> Thanks Daniel. Just one more question. How is it that the stripped bond
> parameters are still there but not used? Is there some kind of flag telling
> pmemd (or sander) not to use them?
>
Ahh, the beauty of the Amber topology file format.
There are 2 sections -- BONDS_INC_HYDROGEN and BONDS_WITHOUT_HYDROGEN
(whose contents contain the information described by the flag names).
These sections contain 3 numbers -- the index of each atom involved in the
bond and the index into the arrays with the bond force constants and
equilibrium values. Cpptraj does not touch the BOND_FORCE_CONSTANT or
BOND_EQUIL_VALUE sections (so all of the parameters are present), but it is
certainly possible that some of the bond types will not be referenced by
any of the bonds in the BONDS_INC_HYDROGEN or BONDS_WITHOUT_HYDROGEN.
Ergo, the force constants and equilibrium values are always in the topology
file, but may not actually be pointed to by any of the bonds that are
computed in the bond loop. The exact same ideas carry over to the angle
and dihedral parameters as well.
As a note, ParmEd does actually strip out unused parameters, although both
approaches will give you identical energies (but different topology files).
HTH,
Jason
> Ignacio
>
>
> On Tue, Mar 26, 2013 at 10:34 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > Hi,
> >
> > As of AmberTools 12 cpptraj will write out a fully functional stripped
> > topology file. Any interactions involving stripped atoms are also
> > removed, although the parameters are still there (they are just not
> > accessed).
> >
> > Note that parmed.py also allows you to strip topologies.
> >
> > -Dan
> >
> > On Tue, Mar 26, 2013 at 8:25 AM, Ignacio J. General <ijgeneral.gmail.com
> >
> > wrote:
> > > Dear Amber users:
> > >
> > > I remember that sometime ago cpptraj was able to strip atoms from the
> > > prmtop file, but it was suggested that we use that only for
> visualization
> > > purposes, not for simulations. Is this still the case? Or I can use a
> > > stripped prmtop for simulations?
> > >
> > > And in case I can use it for MD, when I strip some residue in a
> protein,
> > do
> > > I need to first remove the bonds connecting that residue to the others,
> > or
> > > is this done automatically by cpptraj?
> > >
> > > Thanks,
> > >
> > > Ignacio
> > > _______________________________________________
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> > > 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 201
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-9119 (Fax)
> >
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Mar 26 2013 - 08:00:06 PDT
