Regarding the second question which Ignacio had asked in the beginning: I
think, that running MD with a striped topology and coordinate files will
not be sensible (unless you are stripping only isolated atoms like waters,
ligands or a complete peptide chain). Terminal atoms in such topology
files might have incomplete valencies and hence such MD simulation will be
physically/chemically meaningless.
On Tue, Mar 26, 2013 at 8:20 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
> > > > _______________________________________________
> > > > 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 201
> > > Salt Lake City, UT 84112-5820
> > > http://home.chpc.utah.edu/~cheatham/
> > > (801) 587-9652
> > > (801) 585-9119 (Fax)
> > >
> > > _______________________________________________
> > > 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
>
--
With regards
Vaibhav A. Dixit
Ph.D.
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408, +91-7709129400.
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 26 2013 - 21:00:03 PDT
